diff --git a/BioArchLinux/trinityrnaseq/PKGBUILD b/BioArchLinux/trinityrnaseq/PKGBUILD index 1c792ee377..4566151a41 100644 --- a/BioArchLinux/trinityrnaseq/PKGBUILD +++ b/BioArchLinux/trinityrnaseq/PKGBUILD @@ -11,15 +11,13 @@ url="https://github.com/Trinotate/Trinotate/wiki" license=('BSD-3-Clause') arch=('x86_64') makedepends=('git' 'cmake' 'make' 'python' 'rsync') -source=("git+https://github.com/trinityrnaseq/trinityrnaseq.git#tag=$_pkgname-v$pkgver" - "string.patch") -sha256sums=('3764a52e34eacdf4affc1ab719901e90c68e326b9be7b70a8bacdb8843e0aedf' - '9304eae411d76a6ce1846ed06e7311b35175638a74ec6277909ef9d4ba71769b') +source=("git+https://github.com/trinityrnaseq/trinityrnaseq.git#tag=$_pkgname-v$pkgver") +sha256sums=('3764a52e34eacdf4affc1ab719901e90c68e326b9be7b70a8bacdb8843e0aedf') prepare(){ cd $srcdir/$pkgname git submodule update --init --recursive - patch -p1 < $srcdir/string.patch +# patch -p1 < $srcdir/string.patch } build() { @@ -29,7 +27,8 @@ build() { } package_trinityrnaseq() { - depends=('perl' 'bash' 'glibc' 'java-runtime' 'python' 'zlib') + depends=('perl' 'bash' 'glibc' 'java-runtime' 'python' 'zlib' + 'parafly' 'samtools' 'jellyfish' 'bowtie2' 'salmon') # 'xz' 'bzip2' 'curl' set -x cd $srcdir/trinityrnaseq diff --git a/BioArchLinux/trinityrnaseq/analist b/BioArchLinux/trinityrnaseq/analist new file mode 100644 index 0000000000..8172becc4d --- /dev/null +++ b/BioArchLinux/trinityrnaseq/analist @@ -0,0 +1,124 @@ +Analysis/DifferentialExpression/DE_graph_to_dot.pl +Analysis/DifferentialExpression/DTE_to_DTU.pl +Analysis/DifferentialExpression/GOplot.Rscript +Analysis/DifferentialExpression/Glimma.Trinity.Rscript +Analysis/DifferentialExpression/PtR +Analysis/DifferentialExpression/ROKU.pl +Analysis/DifferentialExpression/add_annot_to_trans_id.pl +Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R +Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl +Analysis/DifferentialExpression/analyze_diff_expr.pl +Analysis/DifferentialExpression/assign_tissue_specific.pl +Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl +Analysis/DifferentialExpression/cut_tree_into_clusters.pl +Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl +Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl +Analysis/DifferentialExpression/diff_express.cgi +Analysis/DifferentialExpression/downsample_count_matrix.pl +Analysis/DifferentialExpression/extract_GO_enriched_genes.pl +Analysis/DifferentialExpression/filter_diff_expr.pl +Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl +Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl +Analysis/DifferentialExpression/get_transcript_lengths.pl +Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl +Analysis/DifferentialExpression/log2_transform_matrix.pl +Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl +Analysis/DifferentialExpression/matrix_to_gene_plots.pl +Analysis/DifferentialExpression/merge_matrices.pl +Analysis/DifferentialExpression/merge_subclusters.pl +Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript +Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript +Analysis/DifferentialExpression/plot_expression_patterns.pl +Analysis/DifferentialExpression/plot_log2FC_hist.Rscript +Analysis/DifferentialExpression/prep_n_run_GOplot.pl +Analysis/DifferentialExpression/prune_isoforms_fasta.pl +Analysis/DifferentialExpression/prune_isoforms_gtf.pl +Analysis/DifferentialExpression/rank_roku_by_expr.pl +Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl +Analysis/DifferentialExpression/rename_matrix_column_labels.pl +Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl +Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl +Analysis/DifferentialExpression/run_DE_analysis.pl +Analysis/DifferentialExpression/run_GOseq.pl +Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl +Analysis/DifferentialExpression/stratify_diff_expression.pl +Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl +Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl +Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl +Analysis/DifferentialExpression/validate_UP_subset.Rscript +Analysis/DifferentialExpression/R/edgeR.TMM.minimal.R +Analysis/DifferentialExpression/R/edgeR_funcs.R +Analysis/DifferentialExpression/R/get_cluster_info.R +Analysis/DifferentialExpression/R/heatmap.3.R +Analysis/DifferentialExpression/R/jaccard_distance.R +Analysis/DifferentialExpression/R/manually_define_clusters.R +Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R +Analysis/DifferentialExpression/R/pairs3.R +Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R +Analysis/DifferentialExpression/R/test.heatmap.3.R +Analysis/DifferentialExpression/R/vioplot2.R +Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R +Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl +Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl +Analysis/DifferentialExpression/TissueEnrichment/README.md +Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl +Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl +Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz +Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl +Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt +Analysis/DifferentialExpression/cluster_sample_data/runMe.sh +Analysis/DifferentialExpression/cluster_sample_data/samples.txt +Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix +Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl +Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl +Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl +Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl +Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl +Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl +Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl +Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl +Analysis/DifferentialExpression/pairwise_summaries/notes +Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl +Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl +Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl +Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl +Analysis/FL_reconstruction_analysis/compute_oracle.pl +Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl +Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl +Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl +Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl +Analysis/FL_reconstruction_analysis/oracle_counter.pl +Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl +Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl +Analysis/FL_reconstruction_analysis/R/boot.tree.R +Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl +Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl +Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl +Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl +Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl +Analysis/SuperTranscripts/README.md +Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py +Analysis/SuperTranscripts/extract_supertranscript_from_reference.py +Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl +Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py +Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl +Analysis/SuperTranscripts/DTU/README.md +Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl +Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl +Analysis/SuperTranscripts/_misc/aln_before_after.pl +Analysis/SuperTranscripts/pylib/Compact_graph_partial.py +Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py +Analysis/SuperTranscripts/pylib/Compact_graph_whole.py +Analysis/SuperTranscripts/pylib/DP_matrix.py +Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py +Analysis/SuperTranscripts/pylib/GraphCycleException.py +Analysis/SuperTranscripts/pylib/Node_alignment.py +Analysis/SuperTranscripts/pylib/Node_path.py +Analysis/SuperTranscripts/pylib/Splice_model_refiner.py +Analysis/SuperTranscripts/pylib/TGLOBALS.py +Analysis/SuperTranscripts/pylib/TGraph.py +Analysis/SuperTranscripts/pylib/TNode.py +Analysis/SuperTranscripts/pylib/Topological_sort.py +Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py +Analysis/SuperTranscripts/pylib/Trinity_util.py +Analysis/SuperTranscripts/pylib/__init__.py diff --git a/BioArchLinux/trinityrnaseq/analist.arch b/BioArchLinux/trinityrnaseq/analist.arch new file mode 100644 index 0000000000..6d28f062f3 --- /dev/null +++ b/BioArchLinux/trinityrnaseq/analist.arch @@ -0,0 +1,123 @@ +Analysis/Compact_graph_partial.py +Analysis/Compact_graph_pruner.py +Analysis/Compact_graph_whole.py +Analysis/DE_graph_to_dot.pl +Analysis/DE_pair_counts_to_matrix.pl +Analysis/DE_results_to_pairwise_summary.pl +Analysis/DP_matrix.py +Analysis/DTE_to_DTU.pl +Analysis/EBSeq_to_pairwise_summary.pl +Analysis/FL_trans_analysis_pipeline.pl +Analysis/GOplot.Rscript +Analysis/Gene_splice_modeler.py +Analysis/Glimma.Trinity.Rscript +Analysis/GraphCycleException.py +Analysis/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz +Analysis/Node_alignment.py +Analysis/Node_path.py +Analysis/PtR +Analysis/README.md +Analysis/ROKU.pl +Analysis/Splice_model_refiner.py +Analysis/TGLOBALS.py +Analysis/TGraph.py +Analysis/TNode.py +Analysis/Topological_sort.py +Analysis/Trinity_fasta_parser.py +Analysis/Trinity_gene_splice_modeler.py +Analysis/Trinity_util.py +Analysis/VCF_to_annotated_SNP_report.pl +Analysis/__init__.py +Analysis/add_annot_to_trans_id.pl +Analysis/add_annotations_to_GO_and_lengths_file.R +Analysis/add_blastx_hit_to_trinity_id.pl +Analysis/add_counts_to_classes.pl +Analysis/aln_before_after.pl +Analysis/analyze_diff_expr.pl +Analysis/assign_tissue_specific.pl +Analysis/blat_full_length_mappings.pl +Analysis/blat_map_filter_with_isoforms.pl +Analysis/blat_psl_to_align_summary_stats.pl +Analysis/blat_query_top_hit_extractor.pl +Analysis/blat_top_tier_genes.pl +Analysis/boot.tree.R +Analysis/class_to_separate_fpkm_matrices.pl +Analysis/clean_bam.pl +Analysis/cleanme.pl +Analysis/compare_gene_trans_DE_ranks.pl +Analysis/compute_oracle.pl +Analysis/count_by_expression_quintile.pl +Analysis/cut_tree_into_clusters.pl +Analysis/define_clusters_by_cutting_tree.pl +Analysis/dexseq_wrapper.pl +Analysis/diff_expr_analysis_to_heatmap_html.pl +Analysis/diff_express.cgi +Analysis/downsample_count_matrix.pl +Analysis/edgeR.TMM.minimal.R +Analysis/edgeR_funcs.R +Analysis/edgeR_to_pairwise_summary.pl +Analysis/es.mef.fpkm.matrix +Analysis/examine_rank_correlation.pl +Analysis/extract_GO_enriched_genes.pl +Analysis/extract_supertranscript_from_reference.py +Analysis/extract_venn_agree_from_summaries.pl +Analysis/filter_diff_expr.pl +Analysis/filter_matrix_min_sum_rowcounts.pl +Analysis/fusion_comparisons_via_maps_files.pl +Analysis/get_cluster_info.R +Analysis/get_genes_from_maps_file.pl +Analysis/get_tissue_enriched_DE_one_vs_all.pl +Analysis/get_transcript_lengths.pl +Analysis/group_isoforms_by_tissue_enrichment.pl +Analysis/heatmap.3.R +Analysis/identify_diff_isoform_splicing.pl +Analysis/jaccard_distance.R +Analysis/log2_transform_matrix.pl +Analysis/log2_transform_median_center_fpkm_matrix.pl +Analysis/manually_define_clusters.R +Analysis/maps_file_to_paralog_representation.pl +Analysis/matrix_to_gene_plots.pl +Analysis/merge_matrices.pl +Analysis/merge_subclusters.pl +Analysis/misc_rnaseq_funcs.R +Analysis/mmdiff_to_pairwise_summary.pl +Analysis/notes +Analysis/oracle_counter.pl +Analysis/orig.samples.txt +Analysis/pairs3.R +Analysis/pairwise_DE_summary_to_DE_classification.pl +Analysis/plot_all_DE_MAplots.Rscript +Analysis/plot_all_DE_volcanos.Rscript +Analysis/plot_expression_patterns.pl +Analysis/plot_log2FC_hist.Rscript +Analysis/prep_n_run_GOplot.pl +Analysis/prune_isoforms_fasta.pl +Analysis/prune_isoforms_gtf.pl +Analysis/rank_roku_by_expr.pl +Analysis/reformat_featureCounts.pl +Analysis/remove_batch_effects_from_count_matrix.pl +Analysis/rename_matrix_column_labels.pl +Analysis/rename_matrix_feature_identifiers.pl +Analysis/replicates_to_sample_averages_matrix.pl +Analysis/rnaseq_plot_funcs.R +Analysis/runMe.sh +Analysis/run_DE_analysis.pl +Analysis/run_GOseq.pl +Analysis/run_TMM_normalization_write_FPKM_matrix.pl +Analysis/run_variant_calling.py +Analysis/samples.txt +Analysis/stratify_diff_expression.pl +Analysis/subcluster_to_canvasXpress_html.make_index_html.pl +Analysis/subcluster_to_canvasXpress_html.pl +Analysis/summarize_diff_expr_across_min_threshold_ranges.pl +Analysis/test.heatmap.3.R +Analysis/test.html +Analysis/test_heatmap_w_pca.R +Analysis/test_session.html +Analysis/tier_gene_trans_alignments.pl +Analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl +Analysis/trinity_to_genomeview_html.pl +Analysis/validate_UP_subset.Rscript +Analysis/venn_pairwise_summaries.pair_stats.pl +Analysis/venn_pairwise_summaries.pl +Analysis/vioplot2.R diff --git a/BioArchLinux/trinityrnaseq/archlist b/BioArchLinux/trinityrnaseq/archlist new file mode 100644 index 0000000000..dfbc7e1149 --- /dev/null +++ b/BioArchLinux/trinityrnaseq/archlist @@ -0,0 +1,505 @@ +Analysis/Compact_graph_partial.py +Analysis/Compact_graph_pruner.py +Analysis/Compact_graph_whole.py +Analysis/DE_graph_to_dot.pl +Analysis/DE_pair_counts_to_matrix.pl +Analysis/DE_results_to_pairwise_summary.pl +Analysis/DP_matrix.py +Analysis/DTE_to_DTU.pl +Analysis/EBSeq_to_pairwise_summary.pl +Analysis/FL_trans_analysis_pipeline.pl +Analysis/GOplot.Rscript +Analysis/Gene_splice_modeler.py +Analysis/Glimma.Trinity.Rscript +Analysis/GraphCycleException.py +Analysis/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz +Analysis/Node_alignment.py +Analysis/Node_path.py +Analysis/PtR +Analysis/README.md +Analysis/ROKU.pl +Analysis/Splice_model_refiner.py +Analysis/TGLOBALS.py +Analysis/TGraph.py +Analysis/TNode.py +Analysis/Topological_sort.py +Analysis/Trinity_fasta_parser.py +Analysis/Trinity_gene_splice_modeler.py +Analysis/Trinity_util.py +Analysis/VCF_to_annotated_SNP_report.pl +Analysis/__init__.py +Analysis/add_annot_to_trans_id.pl +Analysis/add_annotations_to_GO_and_lengths_file.R +Analysis/add_blastx_hit_to_trinity_id.pl +Analysis/add_counts_to_classes.pl +Analysis/aln_before_after.pl +Analysis/analyze_diff_expr.pl +Analysis/assign_tissue_specific.pl +Analysis/blat_full_length_mappings.pl +Analysis/blat_map_filter_with_isoforms.pl +Analysis/blat_psl_to_align_summary_stats.pl +Analysis/blat_query_top_hit_extractor.pl +Analysis/blat_top_tier_genes.pl +Analysis/boot.tree.R +Analysis/class_to_separate_fpkm_matrices.pl +Analysis/clean_bam.pl +Analysis/cleanme.pl +Analysis/compare_gene_trans_DE_ranks.pl +Analysis/compute_oracle.pl +Analysis/count_by_expression_quintile.pl +Analysis/cut_tree_into_clusters.pl +Analysis/define_clusters_by_cutting_tree.pl +Analysis/dexseq_wrapper.pl +Analysis/diff_expr_analysis_to_heatmap_html.pl +Analysis/diff_express.cgi +Analysis/downsample_count_matrix.pl +Analysis/edgeR.TMM.minimal.R +Analysis/edgeR_funcs.R +Analysis/edgeR_to_pairwise_summary.pl +Analysis/es.mef.fpkm.matrix +Analysis/examine_rank_correlation.pl +Analysis/extract_GO_enriched_genes.pl +Analysis/extract_supertranscript_from_reference.py +Analysis/extract_venn_agree_from_summaries.pl +Analysis/filter_diff_expr.pl +Analysis/filter_matrix_min_sum_rowcounts.pl +Analysis/fusion_comparisons_via_maps_files.pl +Analysis/get_cluster_info.R +Analysis/get_genes_from_maps_file.pl +Analysis/get_tissue_enriched_DE_one_vs_all.pl +Analysis/get_transcript_lengths.pl +Analysis/group_isoforms_by_tissue_enrichment.pl +Analysis/heatmap.3.R +Analysis/identify_diff_isoform_splicing.pl +Analysis/jaccard_distance.R +Analysis/log2_transform_matrix.pl +Analysis/log2_transform_median_center_fpkm_matrix.pl +Analysis/manually_define_clusters.R +Analysis/maps_file_to_paralog_representation.pl +Analysis/matrix_to_gene_plots.pl +Analysis/merge_matrices.pl +Analysis/merge_subclusters.pl +Analysis/misc_rnaseq_funcs.R +Analysis/mmdiff_to_pairwise_summary.pl +Analysis/notes +Analysis/oracle_counter.pl +Analysis/orig.samples.txt +Analysis/pairs3.R +Analysis/pairwise_DE_summary_to_DE_classification.pl +Analysis/plot_all_DE_MAplots.Rscript +Analysis/plot_all_DE_volcanos.Rscript +Analysis/plot_expression_patterns.pl +Analysis/plot_log2FC_hist.Rscript +Analysis/prep_n_run_GOplot.pl +Analysis/prune_isoforms_fasta.pl +Analysis/prune_isoforms_gtf.pl +Analysis/rank_roku_by_expr.pl +Analysis/reformat_featureCounts.pl +Analysis/remove_batch_effects_from_count_matrix.pl +Analysis/rename_matrix_column_labels.pl +Analysis/rename_matrix_feature_identifiers.pl +Analysis/replicates_to_sample_averages_matrix.pl +Analysis/rnaseq_plot_funcs.R +Analysis/runMe.sh +Analysis/run_DE_analysis.pl +Analysis/run_GOseq.pl +Analysis/run_TMM_normalization_write_FPKM_matrix.pl +Analysis/run_variant_calling.py +Analysis/samples.txt +Analysis/stratify_diff_expression.pl +Analysis/subcluster_to_canvasXpress_html.make_index_html.pl +Analysis/subcluster_to_canvasXpress_html.pl +Analysis/summarize_diff_expr_across_min_threshold_ranges.pl +Analysis/test.heatmap.3.R +Analysis/test.html +Analysis/test_heatmap_w_pca.R +Analysis/test_session.html +Analysis/tier_gene_trans_alignments.pl +Analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl +Analysis/trinity_to_genomeview_html.pl +Analysis/validate_UP_subset.Rscript +Analysis/venn_pairwise_summaries.pair_stats.pl +Analysis/venn_pairwise_summaries.pl +Analysis/vioplot2.R +PerlLib/ +PerlLib/AlignGraph.pm +PerlLib/AlignNode.pm +PerlLib/Alignment_segment.pm +PerlLib/Alternative_splice_comparer.pm +PerlLib/Ascii_genome_illustrator.pm +PerlLib/BED_utils.pm +PerlLib/BHStats.pm +PerlLib/CDNA_alignment.pm +PerlLib/CDNA_stitcher.pm +PerlLib/CIGAR.pm +PerlLib/CMD_processor.pm +PerlLib/COMMON.pm +PerlLib/ColorGradient.pm +PerlLib/DelimParser.pm +PerlLib/EM.pm +PerlLib/Exons_to_geneobj.pm +PerlLib/Fasta_reader.pm +PerlLib/Fasta_retriever.pm +PerlLib/Fastq_reader.pm +PerlLib/GFF3_alignment_utils.pm +PerlLib/GFF3_utils.pm +PerlLib/GFF_maker.pm +PerlLib/GTF.pm +PerlLib/GTF_utils.pm +PerlLib/Gene_obj.pm +PerlLib/Gene_obj_alignment_assembler.pm +PerlLib/Gene_obj_indexer.pm +PerlLib/GenericGraph.pm +PerlLib/GenericNode.pm +PerlLib/Genome_based_cDNA_assembler.pm +PerlLib/Genome_based_cDNA_graph_assembler.pm +PerlLib/Heatmap.pm +PerlLib/KmerGraph.pm +PerlLib/KmerNode.pm +PerlLib/Ktree.pm +PerlLib/Longest_orf.pm +PerlLib/Nuc_translator.pm +PerlLib/Overlap_assembler.pm +PerlLib/Overlap_info.pm +PerlLib/Overlap_piler.pm +PerlLib/PASA_alignment_assembler.pm +PerlLib/PSL_parser.pm +PerlLib/Pipeliner.pm +PerlLib/Process_cmd.pm +PerlLib/ReadCoverageGraph.pm +PerlLib/ReadCoverageNode.pm +PerlLib/ReadManager.pm +PerlLib/ReadTracker.pm +PerlLib/SAM_entry.pm +PerlLib/SAM_reader.pm +PerlLib/SAM_to_AlignGraph.pm +PerlLib/SingleLinkageClusterer.pm +PerlLib/Splice_graph_assembler.pm +PerlLib/StringGraph.pm +PerlLib/StringNode.pm +PerlLib/Thread_helper.pm +PerlLib/TiedHash.pm +PerlLib/Uniform_Read_Generator.pm +PerlLib/VCF_parser.pm +PerlLib/WigParser.pm +PerlLib/overlapping_nucs.ph +PerlLib/test_Fasta_retriever.pl +PerlLib/test_htc_gridrunner_LSF.pl +PerlLib/test_htc_gridrunner_SGE.pl +PyLib/ +PyLib/Pipeliner.py +Trinity +trinity-plugins/ +trinity-plugins/COLLECTL/ +trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl +trinity-plugins/COLLECTL/util/ +trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py +trinity-plugins/COLLECTL/util/plot_time_vs_resource.Rscript +trinity-plugins/DEXseq_util/ +trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py +trinity-plugins/bamsifter/ +trinity-plugins/bamsifter/bamsifter +util/ +util/ButterflyFastaToGraphDot.pl +util/ExitTester.jar +util/GG_partitioned_trinity_aggregator.pl +util/HiCpipe_nameSortedSam_to_raw.pl +util/Monarch +util/N50.pl +util/N50stats.pl +util/README +util/SAM_coordSorted_fragment_Read_coverage_writer.pl +util/SAM_coordSorted_fragment_coverage_writer2.pl +util/SAM_coordsorted_max_reads_per_position.pl +util/SAM_extract_properly_mapped_pairs.pl +util/SAM_extract_uniquely_mapped_reads.pl +util/SAM_filter_out_unmapped_reads.pl +util/SAM_intron_extractor.pl +util/SAM_nameSorted_to_uniq_count_stats.pl +util/SAM_ordered_pair_jaccard.pl +util/SAM_pair_to_bed.pl +util/SAM_set_transcribed_orient_info.pl +util/SAM_show_alignment.pl +util/SAM_show_alignment.summarize_stats.pl +util/SAM_sortAny_to_count_stats.pl +util/SAM_strand_separator.pl +util/SAM_toString.pl +util/SAM_to_bed.pl +util/SAM_to_fasta.pl +util/SAM_to_frag_coords.pl +util/SAM_to_gff3.minimap2.pl +util/SRA_to_fastq.notes +util/SRA_to_fastq.pl +util/STAR_align_log_parser.py +util/SegmentGraph.pm +util/TPM_weighted_gene_length.py +util/TRINITY.CONFIG.template +util/TophatCufflinksWrapper.pl +util/TrinityStats.pl +util/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl +util/Trinity_node_seq_extractor.pl +util/abundance_estimates_to_matrix.pl +util/acc_list_to_fasta_entries.pl +util/add_LR_reads_to_iworm_bundle.pl +util/alexie_analyze_blast.pl +util/align_and_estimate_abundance.pl +util/align_reads_launch_igv.pl +util/allele_simulator.pl +util/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl +util/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl +util/analyze_blastPlus_topHit_coverage.extract_OS.pl +util/analyze_blastPlus_topHit_coverage.org_matrix.pl +util/analyze_blastPlus_topHit_coverage.pl +util/annotate_chrysalis_welds_with_iworm_names.pl +util/assess_intron_path_sensitivity.pl +util/assess_intron_path_sensitivity.summarizer.pl +util/audit_summary_stats.pl +util/audit_summary_stats.reexamine.pl +util/average.pl +util/bam_to_cuff.pl +util/batch_cmds.pl +util/blast_outfmt6_group_segments.pl +util/blast_outfmt6_group_segments.to_Markov_Clustering.pl +util/blast_outfmt6_group_segments.tophit_coverage.pl +util/blastn_wrapper.pl +util/blat_sam_add_reads2.pl +util/blat_to_sam.pl +util/blat_top_hit_extractor.pl +util/bowtie2_wrapper.pl +util/capture_orig_n_unmapped_reads.pl +util/cat_require_newlines.pl +util/cdhit_examine_isoforms.pl +util/cdna_fasta_file_to_transcript_gtf.pl +util/check_chrysalis_graph_reciprocal_edges.pl +util/check_fastQ_pair_ordering.pl +util/chrys_graph_to_dot.pl +util/collate_fqs.pl +util/combined_nameSorted_to_dup_pairs_removed.pl +util/compare_FL_stats.pl +util/compare_bflies.pl +util/component_to_graph_dot.pl +util/contig_ExN50_statistic.pl +util/convert_fasta_identifiers_for_FL_analysis.pl +util/count_N50_given_MIN_FPKM_threshold.pl +util/count_features_given_MIN_FPKM_threshold.pl +util/count_iso_per_gene_dist.pl +util/count_matrix_features_given_MIN_TPM_threshold.pl +util/count_number_fasta_seqs.pl +util/count_trans_per_component.pl +util/cuff_gtf_to_bed.pl +util/decode_SAM_flag_value.pl +util/define_SAM_coverage_partitions2.pl +util/define_coverage_partitions.pl +util/describe_SAM_read_flag_info.pl +util/determine_RF_strand_specificity.pl +util/diff_splice_paths.pl +util/eXpress_trans_to_gene_results.pl +util/ensure_coord_sorted_sam.pl +util/ensure_paired_end_bam_file.pl +util/examine_iworm_FL_across_threads.pl +util/examine_strand_specificity.pl +util/examine_weldmer_halves.pl +util/expression_analysis_lib.R +util/extract_bam_reads_per_target_gene.pl +util/extract_bam_reads_per_target_transcript.pl +util/extract_fastQ_pairings.pl +util/extract_reads_per_partition.pl +util/fan_out_fasta_seqs_to_indiv_files.pl +util/fastQ_append_acc.pl +util/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl +util/fastQ_rand_subset.pl +util/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl +util/fastQ_to_fastA.pl +util/fastQ_to_tab.pl +util/fastQ_top_N_records.pl +util/fasta_file_reformatter.pl +util/fasta_filter_by_min_length.pl +util/fasta_find_duplicates.pl +util/fasta_remove_duplicates.pl +util/fasta_seq_length.pl +util/fasta_to_cmd_generator.pl +util/fasta_to_tab.pl +util/fasta_write_sense_n_anti.pl +util/fastq_cleaner.pl +util/fastq_interleave_pairs.pl +util/fastq_merge_sorted_tab_lists.pl +util/fastq_stats.pl +util/fastq_unweave_pairs.pl +util/filter_iworm_by_min_length_or_cov.pl +util/filter_low_expr_transcripts.pl +util/filter_out_accs_from_fasta.pl +util/filter_similar_seqs_expr_and_strand_aware.pl +util/filter_transcripts_require_min_cov.pl +util/find_pruned_edges_shouldve_kept.pl +util/flattened_gff_n_genome_to_Trinity_emulator.pl +util/frag_boundary_to_wig.pl +util/frag_to_bed.pl +util/fragment_coverage_writer.pl +util/gene_gff3_to_bed_cmds.pl +util/gene_gff3_to_introns.pl +util/gene_to_shared_transcript_content.pl +util/generate_gene_alt_splicing_graphs.pl +util/generate_trans_graphs.pl +util/genome_gff3_to_gene_gff3_partitions.pl +util/genwig.sh +util/genwig2.py +util/get_GC_content_dist.pl +util/get_Poisson_conf_intervals.R +util/get_Trinity_gene_to_trans_map.pl +util/get_longest_isoform_seq_per_trinity_gene.pl +util/get_path_nodes_from_fasta.pl +util/get_welds_from_chrysals_graphFromFasta_out.pl +util/gff3_file_to_cdna.pl +util/gff3_file_utr_coverage_trimmer.pl +util/gff3_to_genome_feature_base_encoding.parse_SAM.pl +util/gff3_to_genome_feature_base_encoding.pl +util/gmap_gff3_chimera_jaccard_analyzer.pl +util/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl +util/gmap_gff3_to_percent_length_stats.pl +util/gmap_native_to_format_converter.pl +util/gmap_to_ref.pl +util/graph_out_to_bfly_cmd.pl +util/gtf_to_bed_format.pl +util/gtf_to_introns.pl +util/harvest_transcripts.pl +util/hicpipe_raw_converter.pl +util/identify_distal_isoform_variations.pl +util/illustrate_ref_comparison.pl +util/inchworm_transcript_splitter.pl +util/info_files_to_eval_cmds.pl +util/insilico_read_normalization.pl +util/intron_barcharter.pl +util/iworm_LR_to_scaff_pairs.pl +util/iworm_welds_to_dot.pl +util/jaccard_fasta_clipper.pl +util/jaccard_sam_pair_refiner.pl +util/jaccard_wig_clipper.pl +util/join_any.pl +util/join_by_left_col.pl +util/join_expr_vals_single_table.pl +util/join_multi_wig_to_graph_plot.pl +util/join_partitions_within_range.pl +util/kallisto_trans_to_gene_results.pl +util/kmer_counter.pl +util/kmer_histo.NormMaxKCov50.txt +util/kmer_histo.all.txt +util/m8_blastclust.pl +util/map_gtf_transcripts_to_genome_annots.pl +util/merge_RSEM_output_to_matrix.pl +util/merge_blast_n_rsem_results.pl +util/merge_pair_and_LR_scaff_links.pl +util/merge_replicate_bams_via_samples_file.pl +util/merge_rsem_n_express_for_compare.pl +util/mpi_iworm_proc_contigs_to_fa.pl +util/nameSorted_SAM_to_FastQ.pl +util/nameSorted_SAM_to_paired_fastq.pl +util/nbkc_merge_left_right_stats.pl +util/nbkc_normalize.pl +util/notes +util/omp_iworm_thread_contigs_to_fa.pl +util/ordered_fragment_coords_to_jaccard.pl +util/organize_data_table_by_trinity_component.pl +util/outfmt6_add_percent_match_length.pl +util/pair_up_fastq_files_1_2.pl +util/pair_up_fastq_files_LeftRight.pl +util/pair_up_fastq_files_R1_R2.pl +util/pairwise_kmer_content_comparer.pl +util/partition_chrysalis_graphs_n_reads.pl +util/partition_target_transcripts.pl +util/partitioned_trinity_aggregator.pl +util/pbs_check.pl +util/plot_ExN50_statistic.Rscript +util/plot_expressed_gene_dist.pl +util/plot_me.R +util/plot_strand_specificity_dist_by_quantile.Rscript +util/plugin_install_tests.sh +util/prep_rnaseq_alignments_for_genome_assisted_assembly.pl +util/print.pl +util/print_butterfly_assemblies.pl +util/print_kmers.pl +util/process_BLAT_alignments.pl +util/process_GMAP_alignments_gff3_chimeras_ok.pl +util/process_minimap2_alignments.pl +util/prop_pair_sam_refiner.pl +util/pslx_to_gff3.pl +util/randomly_mutate_seqs.pl +util/randomly_sample_PE_fastq.pl +util/remove_cntrl_chars.pl +util/rename_fasta_accessions_using_Trinotate_annot_mappings.pl +util/result.pdf +util/retrieve_sequences_from_fasta.pl +util/revcomp_fasta.pl +util/row_to_column.pl +util/run_BLAT_shortReads.pl +util/run_DETONATE.pl +util/run_GSNAP.pl +util/run_HISAT.pl +util/run_HISAT2_via_samples_file.pl +util/run_HiCpipe_bowtie.pl +util/run_STAR.pl +util/run_STAR_via_samples_file.pl +util/run_Stringtie_via_bam_file_list.pl +util/run_TMM_scale_matrix.pl +util/run_TOPHAT.pl +util/run_Trinity_eval.pl +util/run_Trinity_eval.sh +util/run_UpperQuartileNormalization_matrix.pl +util/run_bowtie2.pl +util/run_bwa.pl +util/run_bwasw_trinity.pl +util/run_jellyfish.pl +util/run_read_simulator_per_fasta_entry.pl +util/run_read_simulator_per_gene.pl +util/run_simulate_reads.wgsim.pl +util/run_trimmomatic_qual_trimming.pl +util/run_trinity_WITH_LR.pl +util/run_trinity_no_LR.pl +util/salmon_runner.pl +util/salmon_trans_to_gene_results.pl +util/sample_data_tests.py +util/scaffold_iworm_contigs.pl +util/segment_GFF_partitions.pl +util/seqinfo_refseq_to_dot.pl +util/shuffle.pl +util/sift_bam_max_cov.pl +util/sim_reads.pl +util/sim_single_bubble.pl +util/simulate_illuminaPE_from_transcripts.pl +util/simulate_illuminaPE_from_transcripts.wgsim.pl +util/simulate_reads_sam_and_fa.pl +util/sixFrameTranslation.pl +util/sort_fastq.pl +util/strip_fasta_header.pl +util/tab_to_fastQ.pl +util/tab_to_fasta.pl +util/tblastn_wrapper.pl +util/testUnlimitStacksize.pl +util/test_prep.py +util/tests.py +util/top_blat_sam_extractor.pl +util/trans_gff3_to_bed_cmds.pl +util/transcript_coverage_UTR_trimmer.pl +util/transcript_fasta_to_ORF_pics.pl +util/transcript_gff3_to_bed.pl +util/transdecoder_pep_to_false_fusion_finder.pl +util/trinity_component_distribution.pl +util/trinity_install_tests.sh +util/trinity_installer.py +util/trinity_kill.pl +util/trinity_kill.sh +util/trinity_pbs.cont +util/trinity_pbs.header +util/trinity_pbs.p1 +util/trinity_pbs.p2 +util/trinity_pbs.p3 +util/trinity_pbs.p4a +util/trinity_pbs.p4b +util/trinity_pbs.p5b +util/trinity_pbs.sh +util/trinity_trans_matrix_to_rep_trans_gene_matrix.pl +util/try_estimate_TPM_filtering_threshold.Rscript +util/validate_fastqs.py +util/wig_clip_to_bed.pl +util/write_partitioned_trinity_cmds.pl +util/write_simulate_read_commands.pl +util/write_trin_cmds.pl diff --git a/BioArchLinux/trinityrnaseq/butterfly.patch b/BioArchLinux/trinityrnaseq/butterfly.patch new file mode 100644 index 0000000000..05f3c30a44 --- /dev/null +++ b/BioArchLinux/trinityrnaseq/butterfly.patch @@ -0,0 +1,90 @@ +Description: Updates the main Trinity program to use FHS paths +Author: Michael R. Crusoe +Forwarded: not-needed +Last-Updated: 2015-02-22 + +--- trinityrnaseq.orig/Trinity ++++ trinityrnaseq/Trinity +@@ -381,7 +381,7 @@ + # --bfly_algorithm : assembly algorithm to use. Options: @BFLY_ALGORITHMS + # + # --bfly_opts :additional parameters to pass through to butterfly +-# (see butterfly options: java -jar Butterfly.jar ). ++# (see butterfly options: java -jar /usr/share/java/Butterfly.jar ). + # (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here). + # + # +@@ -1074,7 +1074,7 @@ + } + + unless ($BFLY_JAR) { +- $BFLY_JAR = "$BUTTERFLY_DIR/Butterfly.jar"; ++ $BFLY_JAR = "/usr/share/java/Butterfly.jar"; + } + + +--- trinityrnaseq.orig/Chrysalis/analysis/Chrysalis.cc ++++ trinityrnaseq/Chrysalis/analysis/Chrysalis.cc +@@ -258,7 +258,7 @@ + commandArg iwormStringCmmd("-iworm","inchworm file", ""); + commandArg oStringCmmd("-o","output directory"); + commandArg pairsStringCmmd("-paired", "paired-end reads are used.", false); +- commandArg butterflyCmmd("-butterfly","butterfly executable", "../Butterfly/Butterfly.jar"); ++ commandArg butterflyCmmd("-butterfly","butterfly executable", "/usr/share/java/Butterfly.jar"); + commandArg skipCmmd("-skip","skip initial 2 steps", false); + commandArg strandCmmd("-strand","strand-specific data", false); + commandArg nobreakCmmd("-nobreak","skip breaking", false); +--- trinityrnaseq.orig/trinity-plugins/bamsifter/Makefile ++++ trinityrnaseq/trinity-plugins/bamsifter/Makefile +@@ -3,7 +3,7 @@ + cwd = $(shell pwd) + + sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h +- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts ++ $(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts + + + htslib/version.h : +--- trinityrnaseq.orig/util/misc/bam_gene_tests/write_trin_cmds.pl ++++ trinityrnaseq/util/misc/bam_gene_tests/write_trin_cmds.pl +@@ -23,7 +23,7 @@ + + # Example: + # +-# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar ~/SVN/trinityrnaseq/trunk/Butterfly/Butterfly.jar --JM 1G --seqType fa ++# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar /usr/share/java/Butterfly.jar --JM 1G --seqType fa + + + __EOUSAGE__ +--- trinityrnaseq.orig/util/misc/compare_bflies.pl ++++ trinityrnaseq/util/misc/compare_bflies.pl +@@ -37,7 +37,7 @@ + my $cmd = "ln -s $comp.reads .; ln -s $comp.out ."; + &process_cmd($cmd); + +- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/prev_vers/Butterfly_r2013_08_14.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt"; ++ $cmd = "java -Xmx4G -jar $/usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt"; + + open (my $ofh, ">bfly.cmd") or die $!; + print $ofh $cmd; +@@ -61,7 +61,7 @@ + &process_cmd($cmd); + + +- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt"; ++ $cmd = "java -Xmx4G -jar /usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt"; + + open (my $ofh, ">bfly.cmd") or die $!; + print $ofh $cmd; +--- trinityrnaseq.orig/util/misc/sim_test_framework/run_Trinity_eval.pl ++++ trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.pl +@@ -17,7 +17,7 @@ + + my $help_flag; + my $ref_trans_fa; +-my $BFLY_JAR = "$ENV{TRINITY_HOME}/Butterfly/Butterfly.jar"; ++my $BFLY_JAR = "/usr/share/java/Butterfly.jar"; + my $INCLUDE_REF_TRANS = 0; + my $OUT_DIR = "testing_dir"; + my $MIN_CONTIG_LENGTH = 200; + diff --git a/BioArchLinux/trinityrnaseq/fix_syspath.patch b/BioArchLinux/trinityrnaseq/fix_syspath.patch new file mode 100644 index 0000000000..17536a64fe --- /dev/null +++ b/BioArchLinux/trinityrnaseq/fix_syspath.patch @@ -0,0 +1,2814 @@ +Description: drop some use of FindBin and hardcode paths +Author: Tim Booth +Forwarded: not-needed +--- a/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl ++++ b/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl +@@ -5,10 +5,9 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + +-use FindBin; + use File::Basename; + +-$ENV{PATH} .= ":$FindBin::RealBin/../../trinity-plugins/slclust/bin/"; ++$ENV{PATH} .= ":/usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/"; + + my $help_flag; + +@@ -87,7 +86,7 @@ if ($help_flag) { + die $usage; + } + +-my $util_dir = "$FindBin::RealBin/util"; ++my $util_dir = "/usr/lib/trinityrnaseq/util"; + + my $found_all_tools = 1; + my @required_tools = qw (blat slclust); +--- a/Trinity ++++ b/Trinity +@@ -5,8 +5,7 @@ use warnings; + use threads; + no strict qw(subs refs); + +-use FindBin; +-use lib ("$FindBin::RealBin/PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use File::Basename; + use Time::localtime; + use Cwd; +@@ -31,7 +30,7 @@ my $ABSOLUTE_MIN_CONTIG_LENGTH = 100; # + + BEGIN { + +- $ENV{TRINITY_HOME} = "$FindBin::RealBin"; ++ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq"; + + } + +@@ -39,16 +38,16 @@ open (STDERR, ">&STDOUT"); ## capturing + + + #directory defnintions +-my $ROOTDIR = "$FindBin::RealBin"; ++my $ROOTDIR = "/usr/lib/trinityrnaseq"; + my $UTILDIR = "$ROOTDIR/util"; + my $MISCDIR = "$UTILDIR/misc"; +-my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/"; +-my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis"; ++my $INCHWORM_DIR = "/usr/bin/"; ++my $CHRYSALIS_DIR = "/usr"; + my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly"; + my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/COLLECTL/collectl"; + my $TRINITY_PLUGINS_DIR = "$ROOTDIR/trinity-plugins"; + my $TRINITY_BIN_DIR = "$TRINITY_PLUGINS_DIR/BIN"; +-my $PARAFLY = "$TRINITY_BIN_DIR/ParaFly"; ++my $PARAFLY = "/usr/bin/ParaFly"; + my $HTSLIB_DIR = "$ROOTDIR/trinity-plugins/htslib"; + + $ENV{LD_LIBRARY_PATH} .= ":${HTSLIB_DIR}"; +@@ -520,7 +519,7 @@ my $usage_synopsis = qq^# + # Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\ + # --genome_guided_max_intron 10000 --CPU 6 + # +-# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/ ++# see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/ + # for sample data and 'runMe.sh' for example Trinity execution + # + # For more details, visit: http://trinityrnaseq.github.io +@@ -3518,11 +3517,7 @@ sub run_genome_guided_Trinity { + if ($long_reads_bam) { + ## add LongReads read group + +- unless ($ENV{PICARD_HOME}) { +- die "Error, for genome-guided long reads pipeline, need env var PICARD_HOME set to the directory where picard.jar is installed"; +- } +- +- my $PICARD_HOME = $ENV{PICARD_HOME}; ++ my $PICARD_HOME = "/usr/share/java"; + + my $pipeliner = new Pipeliner(-verbose => 2); + +--- a/util/align_and_estimate_abundance.pl ++++ b/util/align_and_estimate_abundance.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + + use Cwd; + use Carp; +@@ -418,7 +417,7 @@ main: { + + if ($trinity_mode && ! $gene_trans_map_file) { + $gene_trans_map_file = "$transcripts.gene_trans_map"; +- my $cmd = "$FindBin::RealBin/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file"; + &process_cmd($cmd) unless (-e $gene_trans_map_file); + } + +@@ -824,7 +823,7 @@ sub run_kallisto { + + if ($gene_trans_map_file) { + +- my $cmd = "$FindBin::RealBin/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes"; + &process_cmd($cmd); + } + } +@@ -890,7 +889,7 @@ sub run_salmon { + + if ($gene_trans_map_file) { + +- my $cmd = "$FindBin::RealBin/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes"; + &process_cmd($cmd); + } + }; +--- a/Analysis/DifferentialExpression/ROKU.pl ++++ b/Analysis/DifferentialExpression/ROKU.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use BHStats; + + my $usage = "usage: $0 fpkm.matrix\n\n"; +--- a/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl ++++ b/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + use File::Basename; +-use FindBin; + +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use CanvasXpress::Heatmap; + + +@@ -80,7 +79,7 @@ main: { + + open (my $ofh, ">$R_script") or die "Error, cannot write to file $R_script"; + +- print $ofh "source(\"$FindBin::RealBin/R/get_cluster_info.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/get_cluster_info.R\")\n"; + print $ofh "get_cluster_info(\"$R_data_file\")\n"; + close $ofh; + +--- a/Analysis/DifferentialExpression/get_transcript_lengths.pl ++++ b/Analysis/DifferentialExpression/get_transcript_lengths.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + +--- a/Analysis/DifferentialExpression/merge_matrices.pl ++++ b/Analysis/DifferentialExpression/merge_matrices.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + use Cwd; +-use FindBin; + use File::Basename; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Data::Dumper; + +--- a/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl ++++ b/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + use Cwd; +-use FindBin; + use File::Basename; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Data::Dumper; + +--- a/Analysis/DifferentialExpression/run_DE_analysis.pl ++++ b/Analysis/DifferentialExpression/run_DE_analysis.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use Cwd; +-use FindBin; + use File::Basename; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Data::Dumper; + +@@ -442,7 +441,7 @@ sub run_edgeR_sample_pair { + print $ofh "write.table(rnaseqMatrix, file=\'$output_prefix.edgeR.count_matrix\', sep='\t', quote=F, row.names=T)\n"; + + ## generate MA and Volcano plots +- print $ofh "source(\"$FindBin::RealBin/R/rnaseq_plot_funcs.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R\")\n"; + print $ofh "pdf(\"$output_prefix.edgeR.DE_results.MA_n_Volcano.pdf\")\n"; + + print $ofh "plot_MA_and_Volcano(rownames(result_table), result_table\$logCPM, result_table\$logFC, result_table\$FDR)\n"; +@@ -542,7 +541,7 @@ sub run_DESeq2_sample_pair { + + + ## generate MA and Volcano plots +- print $ofh "source(\"$FindBin::RealBin/R/rnaseq_plot_funcs.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R\")\n"; + print $ofh "pdf(\"$output_prefix.DESeq2.DE_results.MA_n_Volcano.pdf\")\n"; + print $ofh "plot_MA_and_Volcano(rownames(res), log2(res\$baseMean+1), res\$log2FoldChange, res\$padj)\n"; + print $ofh "dev.off()\n"; +@@ -621,7 +620,7 @@ sub run_limma_voom_sample_pair { + + ## generate MA and Volcano plots + print $ofh "# MA and volcano plots\n"; +- print $ofh "source(\"$FindBin::RealBin/R/rnaseq_plot_funcs.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R\")\n"; + print $ofh "pdf(\"$output_prefix.voom.DE_results.MA_n_Volcano.pdf\")\n"; + print $ofh "plot_MA_and_Volcano(rownames(tTags2), tTags2\$logCPM, tTags\$logFC, tTags\$'adj.P.Val')\n"; + print $ofh "dev.off()\n"; +@@ -719,7 +718,7 @@ sub run_ROTS_sample_pair { + + ## generate MA and Volcano plots + print $ofh "# MA and volcano plots\n"; +- print $ofh "source(\"$FindBin::RealBin/R/rnaseq_plot_funcs.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R\")\n"; + print $ofh "pdf(\"$output_prefix.voom.DE_results.MA_n_Volcano.pdf\")\n"; + print $ofh "plot_MA_and_Volcano(rownames(final_table), final_table\$logCPM, final_table\$logFC, final_table\$FDR)\n"; + print $ofh "dev.off()\n"; +--- a/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl ++++ b/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + use Cwd; +-use FindBin; + use File::Basename; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Data::Dumper; + +@@ -104,7 +103,6 @@ sub run_TMM { + + my $tmm_norm_script = "__tmp_runTMM.R"; + open (my $ofh, ">$tmm_norm_script") or die "Error, cannot write to $tmm_norm_script"; +- #print $ofh "source(\"$FindBin::RealBin/R/edgeR_funcs.R\")\n"; + + print $ofh "library(edgeR)\n\n"; + +--- a/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl ++++ b/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl +@@ -3,9 +3,8 @@ + use strict; + use warnings; + +-use FindBin; + use File::Basename; +-use lib ("$ENV{TRINITY_HOME}/PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Process_cmd; + + +--- a/util/misc/Artemis/join_multi_wig_to_graph_plot.pl ++++ b/util/misc/Artemis/join_multi_wig_to_graph_plot.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use WigParser; + + +--- a/util/misc/ButterflyFastaToGraphDot.pl ++++ b/util/misc/ButterflyFastaToGraphDot.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib", "$FindBin::RealBin/../../PerlLib/KmerGraphLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib", "/usr/lib/trinityrnaseq/PerlLib/KmerGraphLib"); + + use Fasta_reader; + use StringGraph; +--- a/util/misc/HiCpipe_nameSortedSam_to_raw.pl ++++ b/util/misc/HiCpipe_nameSortedSam_to_raw.pl +@@ -3,9 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +- +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + use Data::Dumper; +--- a/util/misc/Monarch ++++ b/util/misc/Monarch +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib", "$FindBin::RealBin/../../PerlLib/KmerGraphLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Fasta_reader; + +--- a/util/misc/N50.pl ++++ b/util/misc/N50.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + +--- a/util/misc/SAM_coordsorted_max_reads_per_position.pl ++++ b/util/misc/SAM_coordsorted_max_reads_per_position.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/SAM_intron_extractor.pl ++++ b/util/misc/SAM_intron_extractor.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/misc/SAM_nameSorted_to_uniq_count_stats.pl ++++ b/util/misc/SAM_nameSorted_to_uniq_count_stats.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/SAM_pair_to_bed.pl ++++ b/util/misc/SAM_pair_to_bed.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + use Overlap_piler; +--- a/util/misc/SAM_sortAny_to_count_stats.pl ++++ b/util/misc/SAM_sortAny_to_count_stats.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/SAM_toString.pl ++++ b/util/misc/SAM_toString.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/SAM_to_bed.pl ++++ b/util/misc/SAM_to_bed.pl +@@ -1,10 +1,7 @@ +-#!/usr/bin/env perl +- + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/SAM_to_fasta.pl ++++ b/util/misc/SAM_to_fasta.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + use Nuc_translator; +--- a/util/misc/allele_simulator.pl ++++ b/util/misc/allele_simulator.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib("$FindBin::RealBin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use List::Util qw(min max); + use Data::Dumper; +--- a/util/misc/average.pl ++++ b/util/misc/average.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use BHStats; + + my $count = 0; +--- a/util/misc/blast_outfmt6_group_segments.pl ++++ b/util/misc/blast_outfmt6_group_segments.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib "$FindBin::RealBin/../../PerlLib"; ++use lib "/usr/lib/trinityrnaseq/PerlLib"; + use Fasta_reader; + use List::Util qw(min max); + use Overlap_piler; +--- a/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl ++++ b/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl +@@ -5,8 +5,7 @@ use warnings; + + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); +-use FindBin; +-use lib "$FindBin::RealBin/../../PerlLib"; ++use lib "/usr/lib/trinityrnaseq/PerlLib"; + use Pipeliner; + use File::Basename; + +--- a/util/misc/capture_orig_n_unmapped_reads.pl ++++ b/util/misc/capture_orig_n_unmapped_reads.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Cwd; + use Carp; +--- a/util/misc/cdna_fasta_file_to_transcript_gtf.pl ++++ b/util/misc/cdna_fasta_file_to_transcript_gtf.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Fasta_reader; + +--- a/util/misc/check_fastQ_pair_ordering.pl ++++ b/util/misc/check_fastQ_pair_ordering.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + + my $usage = "usage: $0 left.fq right.fq\n\n"; +--- a/util/misc/contig_ExN50_statistic.pl ++++ b/util/misc/contig_ExN50_statistic.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use File::Basename; + +--- a/util/misc/ensure_paired_end_bam_file.pl ++++ b/util/misc/ensure_paired_end_bam_file.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/misc/extract_fastQ_pairings.pl ++++ b/util/misc/extract_fastQ_pairings.pl +@@ -5,8 +5,7 @@ use warnings; + + use Data::Dumper; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + + my $DEBUG = 0; +--- a/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl ++++ b/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl +@@ -22,8 +22,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + use File::Basename; + +--- a/util/misc/fastQ_rand_subset.pl ++++ b/util/misc/fastQ_rand_subset.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + use File::Basename; + +--- a/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl ++++ b/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl +@@ -22,8 +22,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + use File::Basename; + +--- a/util/misc/fasta_file_reformatter.pl ++++ b/util/misc/fasta_file_reformatter.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 fasta\n"; +--- a/util/misc/fasta_filter_by_min_length.pl ++++ b/util/misc/fasta_filter_by_min_length.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + +--- a/util/misc/fasta_to_cmd_generator.pl ++++ b/util/misc/fasta_to_cmd_generator.pl +@@ -1,8 +1,7 @@ + #!/usr/bin/env perl + + use strict; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Getopt::Std; + use strict; +--- a/util/misc/fasta_write_sense_n_anti.pl ++++ b/util/misc/fasta_write_sense_n_anti.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Nuc_translator; + +--- a/util/misc/fastq_interleave_pairs.pl ++++ b/util/misc/fastq_interleave_pairs.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Fastq_reader; + +--- a/util/misc/fastq_unweave_pairs.pl ++++ b/util/misc/fastq_unweave_pairs.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Fastq_reader; + +--- a/util/misc/gene_gff3_to_introns.pl ++++ b/util/misc/gene_gff3_to_introns.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use Fasta_reader; + use GFF3_utils; +--- a/util/misc/get_longest_isoform_seq_per_trinity_gene.pl ++++ b/util/misc/get_longest_isoform_seq_per_trinity_gene.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + print STDERR "\n\n\tNOTE - longest transcript isn't always the best transcript!... consider filtering based on relative expression support ... \n\n"; +--- a/util/misc/gff3_file_to_cdna.pl ++++ b/util/misc/gff3_file_to_cdna.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use Fasta_reader; + use GFF3_utils; +--- a/util/misc/gff3_file_utr_coverage_trimmer.pl ++++ b/util/misc/gff3_file_utr_coverage_trimmer.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use Fasta_reader; + use GFF3_utils; +--- a/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl ++++ b/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use GFF3_utils; + use SAM_reader; +--- a/util/misc/gff3_to_genome_feature_base_encoding.pl ++++ b/util/misc/gff3_to_genome_feature_base_encoding.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use GFF3_utils; + use Data::Dumper; +--- a/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl ++++ b/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use GFF3_alignment_utils; + use WigParser; + use Data::Dumper; +--- a/util/misc/gmap_gff3_to_percent_length_stats.pl ++++ b/util/misc/gmap_gff3_to_percent_length_stats.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 gmap.gff3 transcripts.fasta\n\n"; +--- a/util/misc/gmap_native_to_format_converter.pl ++++ b/util/misc/gmap_native_to_format_converter.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + + my $usage = "usage: $0 file.gmap (BED|GTF)\n\n"; +--- a/util/misc/gtf_to_bed_format.pl ++++ b/util/misc/gtf_to_bed_format.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + + my $usage = "usage: $0 transcripts.gtf\n\n"; +--- a/util/misc/gtf_to_introns.pl ++++ b/util/misc/gtf_to_introns.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use Fasta_reader; + +--- a/util/misc/identify_distal_isoform_variations.pl ++++ b/util/misc/identify_distal_isoform_variations.pl +@@ -2,9 +2,8 @@ + + use strict; + use warnings; +-use FindBin; + +-use lib ("$FindBin::RealBin/../../PerlLib", "$FindBin::RealBin/PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib", "/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use GFF3_utils; + +--- a/util/misc/illustrate_ref_comparison.pl ++++ b/util/misc/illustrate_ref_comparison.pl +@@ -3,9 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +- +-use lib ("$FindBin::RealBin/../../PerlLib/"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib/"); + use Ascii_genome_illustrator; + use Cwd; + +--- a/util/misc/jaccard_sam_pair_refiner.pl ++++ b/util/misc/jaccard_sam_pair_refiner.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/kmer_counter.pl ++++ b/util/misc/kmer_counter.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + use Carp; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Ktree; + use Nuc_translator; +--- a/util/misc/m8_blastclust.pl ++++ b/util/misc/m8_blastclust.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); +--- a/util/misc/map_gtf_transcripts_to_genome_annots.pl ++++ b/util/misc/map_gtf_transcripts_to_genome_annots.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib/"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib/"); + use Gene_obj; + use GFF3_utils; + use GTF_utils; +--- a/util/misc/merge_blast_n_rsem_results.pl ++++ b/util/misc/merge_blast_n_rsem_results.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 rsem.out blast.outfmt6 [transcripts.fasta]\n\n"; +--- a/util/misc/nameSorted_SAM_to_FastQ.pl ++++ b/util/misc/nameSorted_SAM_to_FastQ.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/misc/nameSorted_SAM_to_paired_fastq.pl ++++ b/util/misc/nameSorted_SAM_to_paired_fastq.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/misc/pairwise_kmer_content_comparer.pl ++++ b/util/misc/pairwise_kmer_content_comparer.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 file.fasta [kmer_length=25]\n\n"; +--- a/util/misc/print_kmers.pl ++++ b/util/misc/print_kmers.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 file.fa [kmer_length=25]\n\n"; +--- a/util/misc/prop_pair_sam_refiner.pl ++++ b/util/misc/prop_pair_sam_refiner.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/randomly_sample_PE_fastq.pl ++++ b/util/misc/randomly_sample_PE_fastq.pl +@@ -10,8 +10,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + use File::Basename; + use List::Util qw(shuffle); +--- a/util/misc/run_HISAT.pl ++++ b/util/misc/run_HISAT.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib("$FindBin::RealBin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Pipeliner; + use File::Basename; + use Cwd; +--- a/util/misc/run_STAR.pl ++++ b/util/misc/run_STAR.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib("$FindBin::RealBin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Pipeliner; + use File::Basename; + use Cwd; +--- a/util/misc/run_STAR_via_samples_file.pl ++++ b/util/misc/run_STAR_via_samples_file.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib("$FindBin::RealBin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Pipeliner; + use File::Basename; + use Cwd; +--- a/util/misc/run_read_simulator_per_fasta_entry.pl ++++ b/util/misc/run_read_simulator_per_fasta_entry.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + +@@ -41,7 +40,7 @@ main: { + + my $outfile = "$sim_out_dir/$outdir/$outdir.reads.fa"; + +- my $cmd = "$FindBin::RealBin/simulate_illuminaPE_from_transcripts.pl --transcripts $template_file --out_prefix $template_file"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/simulate_illuminaPE_from_transcripts.pl --transcripts $template_file --out_prefix $template_file"; + if ($require_proper_pairs_flag) { + $cmd .= " --require_proper_pairs"; + } +--- a/util/misc/simulate_illuminaPE_from_transcripts.pl ++++ b/util/misc/simulate_illuminaPE_from_transcripts.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + use Carp; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Nuc_translator; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); +--- a/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl ++++ b/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + use Carp; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Nuc_translator; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); +@@ -118,9 +117,9 @@ main: { + &process_cmd($cmd); + + # convert to fasta format +- &process_cmd("$FindBin::Bin/../support_scripts/fastQ_to_fastA.pl -I $left_prefix.fq > $left_prefix.fa"); ++ &process_cmd("/usr/lib/trinityrnaseq/util/support_scripts/fastQ_to_fastA.pl -I $left_prefix.fq > $left_prefix.fa"); + +- &process_cmd("$FindBin::Bin/../support_scripts/fastQ_to_fastA.pl -I $right_prefix.fq > $right_prefix.fa"); ++ &process_cmd("/usr/lib/trinityrnaseq/util/support_scripts/fastQ_to_fastA.pl -I $right_prefix.fq > $right_prefix.fa"); + + #unlink("$left_prefix.fq", "$right_prefix.fq"); + +--- a/util/misc/sixFrameTranslation.pl ++++ b/util/misc/sixFrameTranslation.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Nuc_translator; + +--- a/util/misc/sort_fastq.pl ++++ b/util/misc/sort_fastq.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + + my $usage = "usage: $0 file.fastq\n\n"; +--- a/util/misc/strip_fasta_header.pl ++++ b/util/misc/strip_fasta_header.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + use Carp; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 file.fasta\n\n"; +--- a/util/misc/transcript_coverage_UTR_trimmer.pl ++++ b/util/misc/transcript_coverage_UTR_trimmer.pl +@@ -5,9 +5,8 @@ use warnings; + + use threads; + +-use FindBin; + use Getopt::Long qw(:config no_ignore_case bundling); +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use WigParser; + use Fasta_reader; + use Statistics::Descriptive; +@@ -71,7 +70,7 @@ if ($SS_lib_type && $SS_lib_type !~ /^(F + die "Error, invalid --SS_lib_type, only F, R, FR, or RF are possible values"; + } + +-my $UTIL_DIR = "$FindBin::RealBin/"; ++my $UTIL_DIR = "/usr/lib/trinityrnaseq/util/support_scripts"; + + main: { + +--- a/util/misc/transcript_fasta_to_ORF_pics.pl ++++ b/util/misc/transcript_fasta_to_ORF_pics.pl +@@ -1,7 +1,6 @@ + #!/usr/bin/env perl + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use strict; + use warnings; +--- a/util/misc/transcript_gff3_to_bed.pl ++++ b/util/misc/transcript_gff3_to_bed.pl +@@ -3,9 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +- +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + + my $usage = "usage: $0 alignments.gff3\n\n"; +--- a/util/misc/trinity_component_distribution.pl ++++ b/util/misc/trinity_component_distribution.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + use POSIX qw (ceil); +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 Trinity.fasta [length_bin_size=100] [out_prefix='dist']\n\n"; +--- a/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl ++++ b/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl ++++ b/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/SAM_extract_properly_mapped_pairs.pl ++++ b/util/support_scripts/SAM_extract_properly_mapped_pairs.pl +@@ -1,8 +1,7 @@ + #!/usr/bin/env perl + + use strict; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl ++++ b/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl +@@ -1,8 +1,7 @@ + #!/usr/bin/env perl + + use strict; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/SAM_filter_out_unmapped_reads.pl ++++ b/util/support_scripts/SAM_filter_out_unmapped_reads.pl +@@ -1,8 +1,7 @@ + #!/usr/bin/env perl + + use strict; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/SAM_set_transcribed_orient_info.pl ++++ b/util/support_scripts/SAM_set_transcribed_orient_info.pl +@@ -1,8 +1,7 @@ + #!/usr/bin/env perl + + use strict; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/SAM_strand_separator.pl ++++ b/util/support_scripts/SAM_strand_separator.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + use Carp; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + use File::Basename; +--- a/util/support_scripts/SAM_to_frag_coords.pl ++++ b/util/support_scripts/SAM_to_frag_coords.pl +@@ -7,8 +7,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/support_scripts/define_SAM_coverage_partitions2.pl ++++ b/util/support_scripts/define_SAM_coverage_partitions2.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use WigParser; + + my $usage = "usage: $0 strand_coverage.wig strand[+-]\n\n"; +--- a/util/support_scripts/define_coverage_partitions.pl ++++ b/util/support_scripts/define_coverage_partitions.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use WigParser; + + my $usage = "usage: $0 strand_coverage.wig min_coverage strand[+-]\n\n"; +--- a/util/support_scripts/extract_reads_per_partition.pl ++++ b/util/support_scripts/extract_reads_per_partition.pl +@@ -7,8 +7,7 @@ use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use File::Basename; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Nuc_translator; + use SAM_reader; +--- a/util/support_scripts/fastQ_to_fastA.pl ++++ b/util/support_scripts/fastQ_to_fastA.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Nuc_translator; + use IO::Uncompress::Gunzip; + +--- a/util/support_scripts/fasta_to_tab.pl ++++ b/util/support_scripts/fasta_to_tab.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 [multiFastaFile] [NO_FULL_HEADER_FLAG=0]\n\n"; +--- a/util/support_scripts/filter_iworm_by_min_length_or_cov.pl ++++ b/util/support_scripts/filter_iworm_by_min_length_or_cov.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + +--- a/util/support_scripts/fragment_coverage_writer.pl ++++ b/util/support_scripts/fragment_coverage_writer.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/jaccard_fasta_clipper.pl ++++ b/util/support_scripts/jaccard_fasta_clipper.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 transcripts.fasta jaccard_clips.wig\n\n"; +--- a/util/support_scripts/jaccard_wig_clipper.pl ++++ b/util/support_scripts/jaccard_wig_clipper.pl +@@ -6,8 +6,7 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use WigParser; + +--- a/util/support_scripts/ordered_fragment_coords_to_jaccard.pl ++++ b/util/support_scripts/ordered_fragment_coords_to_jaccard.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/support_scripts/run_TMM_scale_matrix.pl ++++ b/util/support_scripts/run_TMM_scale_matrix.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + use Cwd; +-use FindBin; + use File::Basename; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Data::Dumper; + + my $usage = <<__EOUSAGE__; +@@ -67,7 +66,6 @@ sub run_TMM { + + my $tmm_norm_script = "$counts_matrix_file.runTMM.R"; + open (my $ofh, ">$tmm_norm_script") or die "Error, cannot write to $tmm_norm_script"; +- #print $ofh "source(\"$FindBin::RealBin/R/edgeR_funcs.R\")\n"; + + print $ofh "library(edgeR)\n\n"; + +--- a/util/support_scripts/run_UpperQuartileNormalization_matrix.pl ++++ b/util/support_scripts/run_UpperQuartileNormalization_matrix.pl +@@ -5,9 +5,8 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + use Cwd; +-use FindBin; + use File::Basename; +-use lib ("$FindBin::RealBin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Data::Dumper; + + +@@ -76,7 +75,6 @@ sub upper_quartile_normalize { + + my $tmm_norm_script = "__tmp_upper_quart_norm.R"; + open (my $ofh, ">$tmm_norm_script") or die "Error, cannot write to $tmm_norm_script"; +- #print $ofh "source(\"$FindBin::RealBin/R/edgeR_funcs.R\")\n"; + + print $ofh "data = read.table(\"$matrix_file\", header=T, row.names=1, com='')\n"; + print $ofh "get_upper_quartile = function(vec) {\n" +--- a/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl ++++ b/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SingleLinkageClusterer; + use PSL_parser; +@@ -308,7 +307,7 @@ sub examine_blat_mappings { + + my %mappings; + +- my $cmd = "$FindBin::Bin/blat_psl_to_align_summary_stats.pl $blat_output > $blat_output.stats"; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl $blat_output > $blat_output.stats"; + &process_cmd($cmd); + + open(my $fh, "$blat_output.stats") or die "Error, cannot open file $blat_output.stats"; +--- a/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl ++++ b/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use PSL_parser; + use DelimParser; + +--- a/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl ++++ b/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use PSL_parser; + require "overlapping_nucs.ph"; +--- a/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl ++++ b/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl +@@ -7,8 +7,7 @@ use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use File::Basename; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Nuc_translator; + use SAM_reader; +--- a/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl ++++ b/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl +@@ -7,8 +7,7 @@ use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use File::Basename; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Nuc_translator; + use SAM_reader; +--- a/util/misc/blat_util/blat_sam_add_reads2.pl ++++ b/util/misc/blat_util/blat_sam_add_reads2.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Nuc_translator; + + my $usage = "usage: $0 blat.psl.nameSorted.sam reads.tab.nameSorted\n\n"; +--- a/util/misc/blat_util/process_BLAT_alignments.pl ++++ b/util/misc/blat_util/process_BLAT_alignments.pl +@@ -1,7 +1,6 @@ + #!/usr/bin/env perl + +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use strict; + use warnings; +@@ -66,7 +65,6 @@ my $genome_db = $opt_g; + my $transcript_db = $opt_t; + my $output_prefix = $opt_o || "blat"; + my $blat_path = "blat"; +-my $util_dir = $FindBin::RealBin; + + unless ($genome_db && $transcript_db) { + die "$usage\n"; +@@ -171,7 +169,7 @@ my @top_hits_files; + + foreach my $pslx_file (@pslx_files) { + +- my $cmd = "$util_dir/blat_top_hit_extractor.pl $pslx_file $num_top_hits > $pslx_file.top_${num_top_hits}"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/blat_util/blat_top_hit_extractor.pl $pslx_file $num_top_hits > $pslx_file.top_${num_top_hits}"; + + my $completed_checkpoint_file = "$pslx_file.top_${num_top_hits}.completed"; + unless (-e $completed_checkpoint_file) { +@@ -220,7 +218,7 @@ foreach my $top_hits_file (@top_hits_fil + # convert to gff3 format + print STDERR "-converting $top_hits_file to gff3\n"; + +- my $cmd = "$util_dir/pslx_to_gff3.pl < $top_hits_file >> $output_prefix.gff3"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/blat_util/pslx_to_gff3.pl < $top_hits_file >> $output_prefix.gff3"; + &process_cmd($cmd); + } + +--- a/util/misc/blat_util/top_blat_sam_extractor.pl ++++ b/util/misc/blat_util/top_blat_sam_extractor.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use SAM_reader; + use SAM_entry; +--- a/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl ++++ b/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::RealBin/../../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Gene_obj; + use GFF3_utils; + use BED_utils; +--- a/Analysis/DifferentialExpression/prune_isoforms_fasta.pl ++++ b/Analysis/DifferentialExpression/prune_isoforms_fasta.pl +@@ -5,8 +5,7 @@ use warnings; + + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Data::Dumper; + +--- a/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl ++++ b/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl +@@ -6,8 +6,7 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use Fasta_reader; + use Gene_obj; +--- a/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl ++++ b/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Process_cmd; + use File::Basename; + +@@ -15,10 +14,10 @@ my $collectl_dir = $ARGV[0] or die $usag + + main: { + +- my $cmd = "$FindBin::Bin/util/collectl_dat_to_time_matrix.py --dat $collectl_dir/collectl.dat --out_prefix " . basename($collectl_dir); ++ my $cmd = "/usr/lib/trinityrnaseq/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py --dat $collectl_dir/collectl.dat --out_prefix " . basename($collectl_dir); + &process_cmd($cmd); + +- $cmd = "$FindBin::Bin/util/plot_time_vs_resource.Rscript " . basename($collectl_dir); ++ $cmd = "/usr/lib/trinityrnaseq/trinity-plugins/COLLECTL/util/plot_time_vs_resource.Rscript " . basename($collectl_dir); + &process_cmd($cmd); + + exit(0); +--- a/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl ++++ b/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + use Carp; + use Data::Dumper; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SingleLinkageClusterer; + use Overlap_piler; + +--- a/util/misc/align_reads_launch_igv.pl ++++ b/util/misc/align_reads_launch_igv.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib("$FindBin::Bin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Pipeliner; + use Cwd; + +--- a/util/misc/collate_fqs.pl ++++ b/util/misc/collate_fqs.pl +@@ -5,8 +5,7 @@ use warnings; + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); + +-use FindBin; +-use lib("$FindBin::Bin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Fastq_reader; + use Data::Dumper; + +--- a/util/misc/determine_RF_strand_specificity.pl ++++ b/util/misc/determine_RF_strand_specificity.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/misc/examine_strand_specificity.pl ++++ b/util/misc/examine_strand_specificity.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + use Process_cmd; +@@ -81,7 +80,7 @@ main: { + + + ## plot it. +- my $cmd = "$FindBin::Bin/plot_strand_specificity_dist_by_quantile.Rscript $out_prefix.dat"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/plot_strand_specificity_dist_by_quantile.Rscript $out_prefix.dat"; + &process_cmd($cmd); + + +--- a/util/misc/fasta_seq_length.pl ++++ b/util/misc/fasta_seq_length.pl +@@ -2,9 +2,8 @@ + + use strict; + use warnings; +-use FindBin; + +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $usage = "usage: $0 fastaFile\n\n"; +--- a/util/misc/filter_similar_seqs_expr_and_strand_aware.pl ++++ b/util/misc/filter_similar_seqs_expr_and_strand_aware.pl +@@ -5,8 +5,7 @@ use warnings; + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); + use Data::Dumper; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $help_flag; +--- a/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl ++++ b/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Nuc_translator; + use Data::Dumper; +--- a/util/misc/get_GC_content_dist.pl ++++ b/util/misc/get_GC_content_dist.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Process_cmd; + +--- a/util/misc/run_HISAT2_via_samples_file.pl ++++ b/util/misc/run_HISAT2_via_samples_file.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Process_cmd; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use Pipeliner; +--- a/util/misc/run_bowtie2.pl ++++ b/util/misc/run_bowtie2.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Process_cmd; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); + use Carp; +--- a/util/support_scripts/ensure_coord_sorted_sam.pl ++++ b/util/support_scripts/ensure_coord_sorted_sam.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_reader; + use SAM_entry; + +--- a/util/support_scripts/fasta_find_duplicates.pl ++++ b/util/support_scripts/fasta_find_duplicates.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + +--- a/util/support_scripts/filter_transcripts_require_min_cov.pl ++++ b/util/support_scripts/filter_transcripts_require_min_cov.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use DelimParser; + use Carp; +--- a/util/support_scripts/iworm_LR_to_scaff_pairs.pl ++++ b/util/support_scripts/iworm_LR_to_scaff_pairs.pl +@@ -8,8 +8,7 @@ use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); + use Data::Dumper; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $MIN_CONTAINMENT = 96; +--- a/util/support_scripts/nbkc_merge_left_right_stats.pl ++++ b/util/support_scripts/nbkc_merge_left_right_stats.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use DelimParser; + + use Getopt::Long qw(:config no_ignore_case bundling pass_through); +--- a/util/support_scripts/nbkc_normalize.pl ++++ b/util/support_scripts/nbkc_normalize.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use DelimParser; + +--- a/util/support_scripts/outfmt6_add_percent_match_length.pl ++++ b/util/support_scripts/outfmt6_add_percent_match_length.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use List::Util qw(min max); + +--- a/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl ++++ b/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl +@@ -8,9 +8,8 @@ use threads; + + use File::Basename; + use File::Spec; +-use FindBin; + use Getopt::Long qw(:config no_ignore_case bundling); +-use lib("$FindBin::Bin/../../PerlLib"); ++use lib("/usr/lib/trinityrnaseq/PerlLib"); + use Thread_helper; + use Cwd; + +@@ -99,7 +98,7 @@ if ($SS_lib_type && $SS_lib_type !~ /^(F + die "Error, invalid --SS_lib_type, only F, R, FR, or RF are possible values"; + } + +-my $UTIL_DIR = "$FindBin::RealBin/"; ++my $UTIL_DIR = "/usr/lib/trinityrnaseq/util/support_scripts"; + + main: { + +--- a/util/support_scripts/salmon_runner.pl ++++ b/util/support_scripts/salmon_runner.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Process_cmd; + + my $usage = "\n\n\tusage: $0 Trinity.fasta reads.fa [threads=1]\n\n"; +--- a/util/support_scripts/scaffold_iworm_contigs.pl ++++ b/util/support_scripts/scaffold_iworm_contigs.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_entry; + + my $usage = "\n\nusage: $0 nameSorted.sam iworm_fasta_file\n\n"; +--- a/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl ++++ b/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); +-use FindBin; +-use lib "$FindBin::Bin/../../../PerlLib"; ++use lib "/usr/lib/trinityrnaseq/PerlLib"; + use Pipeliner; + use File::Basename; + +@@ -87,7 +86,7 @@ unless ($aligner =~ /^(STAR|HISAT2)$/i) + + $aligner = lc $aligner; + +-my $TRINITY_HOME = "$FindBin::Bin/../../.."; ++my $TRINITY_HOME = "/usr/lib/trinityrnaseq"; + + main: { + +@@ -173,7 +172,7 @@ main: { + $pipeliner->add_commands(new Command($cmd, "$analysis_token.$bam_file.fc.ok")); + + +- $pipeliner->add_commands(new Command("$FindBin::Bin/util/reformat_featureCounts.pl $bam_file.fc > $bam_file.counts", ++ $pipeliner->add_commands(new Command("/usr/lib/trinityrnaseq/Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl $bam_file.fc > $bam_file.counts", + "$analysis_token.$bam_file.counts.ok")); + + push (@counts_files, "$bam_file.counts"); +--- a/Analysis/DifferentialExpression/diff_express.cgi ++++ b/Analysis/DifferentialExpression/diff_express.cgi +@@ -5,10 +5,9 @@ use warnings; + + use CGI; + use CGI::Carp qw(fatalsToBrowser); +-use FindBin; + use File::Basename; + +-use lib ("$FindBin::RealBin/PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + + use CanvasXpress::Heatmap; + use BHStats; +--- a/util/TrinityStats.pl ++++ b/util/TrinityStats.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use BHStats; + +--- a/util/analyze_blastPlus_topHit_coverage.pl ++++ b/util/analyze_blastPlus_topHit_coverage.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib ("$FindBin::RealBin/../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + use Data::Dumper; + +--- a/util/filter_low_expr_transcripts.pl ++++ b/util/filter_low_expr_transcripts.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); +-use FindBin; +-use lib ("$FindBin::RealBin/../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use Fasta_reader; + + my $help_flag; +--- a/util/insilico_read_normalization.pl ++++ b/util/insilico_read_normalization.pl +@@ -5,8 +5,7 @@ use warnings; + use threads; + no strict qw(subs refs); + +-use FindBin; +-use lib ("$FindBin::RealBin/../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use File::Basename; + use Cwd; + use Carp; +@@ -18,7 +17,7 @@ use Data::Dumper; + use COMMON; + use DB_File; + +-$ENV{PATH} = "$FindBin::Bin/../trinity-plugins/BIN:$ENV{PATH}"; ++$ENV{PATH} = "/usr/lib/trinityrnaseq/trinity-plugins/BIN:$ENV{PATH}"; + + + open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream +@@ -118,9 +117,9 @@ _EOUSAGE_ + + ; + +-my $ROOTDIR = "$FindBin::RealBin/../"; ++my $ROOTDIR = "/usr/lib/trinityrnaseq/"; + my $UTILDIR = "$ROOTDIR/util/support_scripts/"; +-my $INCHWORM_DIR = "$ROOTDIR/Inchworm"; ++my $INCHWORM_DIR = "/usr"; + + unless (@ARGV) { + die "$usage\n"; +--- a/util/sift_bam_max_cov.pl ++++ b/util/sift_bam_max_cov.pl +@@ -4,8 +4,7 @@ use strict; + use warnings; + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); +-use FindBin; +-use lib ("$FindBin::Bin/../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use SAM_entry; + + my $help_flag; +--- a/Analysis/DifferentialExpression/PtR ++++ b/Analysis/DifferentialExpression/PtR +@@ -4,7 +4,6 @@ use strict; + use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); +-use FindBin; + use File::Basename; + + my $min_rowSums = 0; +@@ -590,10 +589,10 @@ main: { + + + # source these after potential data restoration above - in case they changed. +- $Rscript .= "source(\"$FindBin::RealBin/R/heatmap.3.R\")\n"; +- $Rscript .= "source(\"$FindBin::RealBin/R/misc_rnaseq_funcs.R\")\n"; +- $Rscript .= "source(\"$FindBin::RealBin/R/pairs3.R\")\n"; +- $Rscript .= "source(\"$FindBin::RealBin/R/vioplot2.R\")\n"; ++ $Rscript .= "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/heatmap.3.R\")\n"; ++ $Rscript .= "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R\")\n"; ++ $Rscript .= "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/pairs3.R\")\n"; ++ $Rscript .= "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/vioplot2.R\")\n"; + + $Rscript .= "data = primary_data\n"; + +--- a/Analysis/DifferentialExpression/analyze_diff_expr.pl ++++ b/Analysis/DifferentialExpression/analyze_diff_expr.pl +@@ -4,7 +4,6 @@ use strict; + use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); +-use FindBin; + use Data::Dumper; + + my $usage = <<__EOUSAGE__; +@@ -237,7 +236,7 @@ main: { + sub cluster_diff_expressed_transcripts { + my ($diff_expr_matrix_file) = @_; + +- my $cmd = "$FindBin::RealBin/PtR -m $diff_expr_matrix_file --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save @ARGV"; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m $diff_expr_matrix_file --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save @ARGV"; + + if ($samples_file) { + $cmd .= " -s $samples_file"; +@@ -406,7 +405,7 @@ sub parse_result_files_find_diffExp { + my $background_file = $result_file; + $background_file =~ s/\.DE_results$/\.count_matrix/ or die "Error, cannot modify $result_file to count_matrix name"; + +- my $cmd = "$FindBin::RealBin/run_GOseq.pl --GO_assignments $GO_annots_file " ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments $GO_annots_file " + . " --lengths $gene_lengths_file --genes_single_factor $condA_up_subset_file" + . " --background $background_file "; + +@@ -419,7 +418,7 @@ sub parse_result_files_find_diffExp { + } + + +- $cmd = "$FindBin::RealBin/run_GOseq.pl --GO_assignments $GO_annots_file " ++ $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments $GO_annots_file " + . " --lengths $gene_lengths_file --genes_single_factor $condB_up_subset_file" + . " --background $background_file "; + +@@ -434,7 +433,7 @@ sub parse_result_files_find_diffExp { + + if ($countA + $countB) { + +- $cmd = "$FindBin::RealBin/run_GOseq.pl --GO_assignments $GO_annots_file " ++ $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments $GO_annots_file " + . " --lengths $gene_lengths_file --genes_single_factor $either_subset_file" + . " --background $background_file "; + +@@ -447,7 +446,7 @@ sub parse_result_files_find_diffExp { + } + + if ($RUN_GOPLOT) { +- $cmd = "$FindBin::RealBin/prep_n_run_GOplot.pl --GO_annots $GO_annots_file " ++ $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/prep_n_run_GOplot.pl --GO_annots $GO_annots_file " + . " --DE_subset $either_subset_file " + . " --DE_GO_enriched $either_subset_file.GOseq.enriched " + . " --tmpdir $either_subset_file.GOseq.enriched.GOplot_dat" +@@ -534,7 +533,7 @@ sub write_matrix_generate_heatmap { + } + close $ofh; + +- my $cmd = "$FindBin::RealBin/PtR -m $matrix_out_file -s $pairwise_samples_file --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean @ARGV "; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m $matrix_out_file -s $pairwise_samples_file --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean @ARGV "; + + if ($samples_file) { + $cmd .= " -s $samples_file "; +--- a/Analysis/DifferentialExpression/cut_tree_into_clusters.pl ++++ b/Analysis/DifferentialExpression/cut_tree_into_clusters.pl +@@ -5,7 +5,6 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use File::Basename; +-use FindBin; + + my $usage = <<__EOUSAGE__; + +@@ -88,7 +87,7 @@ main: { + #print $ofh "library(gplots)\n"; + print $ofh "library(Biobase)\n"; + print $ofh "library(fastcluster)\n"; +- print $ofh "source(\"$FindBin::RealBin/R/heatmap.3.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/heatmap.3.R\")\n"; + + print $ofh "load(\"$R_data_file\")\n"; + +--- a/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl ++++ b/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl +@@ -5,7 +5,6 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use File::Basename; +-use FindBin; + + my $usage = <<__EOUSAGE__; + +@@ -89,7 +88,7 @@ main: { + #print $ofh "library(gplots)\n"; + print $ofh "library(Biobase)\n"; + print $ofh "library(fastcluster)\n"; +- print $ofh "source(\"$FindBin::RealBin/R/heatmap.3.R\")\n"; ++ print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/heatmap.3.R\")\n"; + + print $ofh "load(\"$R_data_file\")\n"; + +@@ -191,7 +190,7 @@ main: { + + chdir $outdir or die "Error, cannot cd into $outdir"; + +- my $cmd = "$FindBin::RealBin/plot_expression_patterns.pl subcluster\*fpkm.matrix"; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/plot_expression_patterns.pl subcluster\*fpkm.matrix"; + &process_cmd($cmd); + + +--- a/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl ++++ b/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl +@@ -4,8 +4,6 @@ use strict; + use warnings; + use Carp; + +-use FindBin; +- + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + + +@@ -101,7 +99,7 @@ main: { + } + + ## generate a heatmap +- my $cmd = "$FindBin::RealBin/PtR -m $fpkm_outfile --log2 --heatmap --gene_dist euclidean --sample_dist euclidean"; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m $fpkm_outfile --log2 --heatmap --gene_dist euclidean --sample_dist euclidean"; + if ($samples_file) { + $cmd .= " -s $samples_file "; + } +--- a/Analysis/DifferentialExpression/prune_isoforms_gtf.pl ++++ b/Analysis/DifferentialExpression/prune_isoforms_gtf.pl +@@ -5,7 +5,6 @@ use warnings; + + use Carp; + use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through); +-use FindBin; + use Data::Dumper; + + my $help_flag; +--- a/Analysis/DifferentialExpression/run_GOseq.pl ++++ b/Analysis/DifferentialExpression/run_GOseq.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + +--- a/Analysis/DifferentialExpression/stratify_diff_expression.pl ++++ b/Analysis/DifferentialExpression/stratify_diff_expression.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + + my $usage = "\n\nusage: $0 edgeR_dir\n\n"; + +@@ -21,7 +20,7 @@ for my $fold_change (1..8) { + + for my $pvalue (2..10) { + +- my $cmd = "$FindBin::RealBin/analyze_diff_expr.pl --matrix $fpkm_matrix_file -C $fold_change -P 1e-$pvalue"; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix $fpkm_matrix_file -C $fold_change -P 1e-$pvalue"; + &process_cmd($cmd); + + +--- a/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl ++++ b/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl +@@ -3,8 +3,7 @@ + use strict; + use warnings; + +-use FindBin; +-use lib("$FindBin::RealBin/../TrinityWeb/cgi-bin/PerlLib/"); ++use lib("/usr/lib/trinityrnaseq/PerlLib/"); + use CanvasXpress::Heatmap; + use CanvasXpress::PlotOnLoader; + use CanvasXpress::Line; +--- a/Analysis/FL_reconstruction_analysis/compute_oracle.pl ++++ b/Analysis/FL_reconstruction_analysis/compute_oracle.pl +@@ -3,8 +3,6 @@ + use strict; + use warnings; + +-use FindBin; +- + my $usage = "usage: $0 reads.fasta ref_transcripts.fasta [SS]\n\n"; + + my $reads_file = $ARGV[0] or die $usage; +@@ -12,7 +10,7 @@ my $ref_transcripts_fasta = $ARGV[1] or + my $SS_flag = $ARGV[2] || 0; + + +-my $cmd = "$FindBin::RealBin/../../Inchworm/bin/inchworm " ++my $cmd = "/usr/bin/inchworm " + . " --reads $reads_file " + . " --checkFastaPath $ref_transcripts_fasta "; + +--- a/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl ++++ b/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + + my $usage = "usage: $0 file.paralog_clusters file.maps\n\n"; + +--- a/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl ++++ b/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + + my $usage = "usage: $0 genes.fasta transcripts.fasta max_intron BLAT_CPU [STRAND-SPECIFIC_FLAG=0]\n\n"; + +@@ -16,14 +15,14 @@ my $SS = $ARGV[4] || 0; + main: { + + ## run blat: +- my $cmd = "$FindBin::RealBin/../../util/process_BLAT_alignments.pl -g $genes_fasta -t $trans_fasta -I $max_intron --CPU $blat_cpu --KEEP_PSLX"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/blat_util/process_BLAT_alignments.pl -g $genes_fasta -t $trans_fasta -I $max_intron --CPU $blat_cpu --KEEP_PSLX"; + + &process_cmd($cmd); + + $cmd = "cat blat_out_dir/*top_1 > blat.top_1.pslx"; + &process_cmd($cmd); + +- $cmd = "$FindBin::RealBin/util/blat_top_tier_genes.pl blat.top_1.pslx $SS"; ++ $cmd = "/usr/lib/trinityrnaseq/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl blat.top_1.pslx $SS"; + &process_cmd($cmd); + + exit(0); +--- a/util/abundance_estimates_to_matrix.pl ++++ b/util/abundance_estimates_to_matrix.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + use File::Basename; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use Carp; +@@ -363,11 +362,11 @@ sub perform_cross_sample_norm { + my ($tpm_matrix_file, $out_prefix_name) = @_; + + if ($cross_sample_norm =~ /^TMM$/i) { +- my $cmd = "$FindBin::RealBin/support_scripts/run_TMM_scale_matrix.pl --matrix $tpm_matrix_file > $out_prefix_name.$cross_sample_norm.EXPR.matrix"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/run_TMM_scale_matrix.pl --matrix $tpm_matrix_file > $out_prefix_name.$cross_sample_norm.EXPR.matrix"; + &process_cmd($cmd); + } + elsif ($cross_sample_norm =~ /^UpperQuartile$/) { +- my $cmd = "$FindBin::RealBin/support_scripts/run_UpperQuartileNormalization_matrix.pl --matrix $tpm_matrix_file > $out_prefix_name.$cross_sample_norm.EXPR.matrix"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/run_UpperQuartileNormalization_matrix.pl --matrix $tpm_matrix_file > $out_prefix_name.$cross_sample_norm.EXPR.matrix"; + &process_cmd($cmd); + } + elsif ($cross_sample_norm =~ /^none$/i) { +--- a/util/misc/TophatCufflinksWrapper.pl ++++ b/util/misc/TophatCufflinksWrapper.pl +@@ -6,7 +6,6 @@ use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + use File::Basename; +-use FindBin; + use Cwd; + + my $usage = <<__EOUSAGE__; +--- a/util/misc/bam_gene_tests/write_trin_cmds.pl ++++ b/util/misc/bam_gene_tests/write_trin_cmds.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + + my $usage = <<__EOUSAGE__; +@@ -70,7 +69,7 @@ while (<$fh>) { + + my $file = pop @x; + +- my $cmd = "$FindBin::RealBin/../../../Trinity --single \"$file\" --output \"$file.trinity.$out_token\" $trin_args "; ++ my $cmd = "/usr/bin/Trinity --single \"$file\" --output \"$file.trinity.$out_token\" $trin_args "; + + print "$cmd\n"; + } +--- a/util/misc/blat_util/blat_to_sam.pl ++++ b/util/misc/blat_util/blat_to_sam.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use Cwd; + + use Getopt::Long qw(:config no_ignore_case bundling); +@@ -72,9 +71,7 @@ unless ($genome_fa && $reads_fa) { + + main: { + +- my $util_dir = "$FindBin::RealBin/../util"; +- +- my $cmd = "$util_dir/fasta_to_tab.pl $reads_fa > $reads_fa.tab"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/fasta_to_tab.pl $reads_fa > $reads_fa.tab"; + &process_cmd($cmd) unless (-s "$reads_fa.tab"); + + $cmd = "sort -T . -S 2G -k 1,1 $reads_fa.tab > $reads_fa.tab.sort"; +@@ -90,11 +87,11 @@ main: { + + + # add the reads +- $cmd = "$util_dir/blat_sam_add_reads2.pl $reads_fa.psl.sam $reads_fa.tab.sort > $reads_fa.psl.sam.wReads"; ++ $cmd = "/usr/lib/trinityrnaseq/util/misc/blat_util/blat_sam_add_reads2.pl $reads_fa.psl.sam $reads_fa.tab.sort > $reads_fa.psl.sam.wReads"; + &process_cmd($cmd); + + ## prune output to top matches: +- $cmd = "$util_dir/top_blat_sam_extractor.pl $reads_fa.psl.sam.wReads $top_hits $min_per_ID > $reads_fa.psl.sam.wReads.top"; ++ $cmd = "/usr/lib/trinityrnaseq/util/misc/blat_util/top_blat_sam_extractor.pl $reads_fa.psl.sam.wReads $top_hits $min_per_ID > $reads_fa.psl.sam.wReads.top"; + &process_cmd($cmd); + + $cmd = "$FindBin::RealBin/cigar_tweaker $reads_fa.psl.sam.wReads.top $genome_fa > $reads_fa.psl.sam.wReads.top.tweaked"; +--- a/util/misc/count_trans_per_component.pl ++++ b/util/misc/count_trans_per_component.pl +@@ -3,8 +3,6 @@ + use strict; + use warnings; + +-use FindBin; +- + my $usage = "usage: $0 bfly.A.fasta [bfly.B.fasta ...]\n\n"; + + my @files = @ARGV or die $usage; +--- a/util/misc/frag_to_bed.pl ++++ b/util/misc/frag_to_bed.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + + use lib ("$ENV{EUK_MODULES}"); + use Gene_obj; +--- a/util/misc/genome_gff3_to_gene_gff3_partitions.pl ++++ b/util/misc/genome_gff3_to_gene_gff3_partitions.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + use lib ("$ENV{TRINITY_HOME}/PerlLib"); + use Gene_obj; + use Fasta_reader; +--- a/util/misc/plot_expressed_gene_dist.pl ++++ b/util/misc/plot_expressed_gene_dist.pl +@@ -3,15 +3,13 @@ + use strict; + use warnings; + +-use FindBin; +- + my $usage = "usage: $0 RSEM.isoforms.fpkm\n\n"; + + my $fpkm_file = $ARGV[0] or die $usage; + + my $Rscript = "$fpkm_file.R"; + open (my $ofh, ">$Rscript"); +-print $ofh "source(\"$FindBin::RealBin/R/expression_analysis_lib.R\")\n"; ++print $ofh "source(\"/usr/lib/trinityrnaseq/util/R/expression_analysis_lib.R\")\n"; + print $ofh "pdf(\"$fpkm_file.genes_vs_minFPKM.pdf\")\n"; + print $ofh "plot_expressed_gene_counts(\"$fpkm_file\", title=\"expressed transcripts vs. min FPKM\", fpkm_range=seq(0,5,0.01), outfile=\"$fpkm_file.genes_vs_minFPKM.dat\")\n"; + print $ofh "dev.off()\n"; +--- a/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl ++++ b/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use File::Basename; + use Cwd; + +--- a/util/misc/run_GSNAP.pl ++++ b/util/misc/run_GSNAP.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use File::Basename; + use Cwd; + +--- a/util/misc/run_HiCpipe_bowtie.pl ++++ b/util/misc/run_HiCpipe_bowtie.pl +@@ -3,9 +3,6 @@ + use strict; + use warnings; + +-use FindBin; +- +- + my $usage = "usage: $0 genome.fasta left.fq right.fq [output_dir]\n\n"; + + my $genome_file = $ARGV[0] or die $usage; +@@ -26,7 +23,7 @@ main: { + . " -- -a -m 1 --best --strata -p 4 --chunkmbs 512 "; + &process_cmd($cmd) unless (-s "$output_dir/$output_dir.nameSorted.sam"); + +- $cmd = "$FindBin::RealBin/HiCpipe_nameSortedSam_to_raw.pl $output_dir/$output_dir.nameSorted.sam > $output_dir/$output_dir.raw"; ++ $cmd = "/usr/lib/trinityrnaseq/util/misc/HiCpipe_nameSortedSam_to_raw.pl $output_dir/$output_dir.nameSorted.sam > $output_dir/$output_dir.raw"; + &process_cmd($cmd) unless (-s "$output_dir/$output_dir.raw"); + + +--- a/util/misc/run_TOPHAT.pl ++++ b/util/misc/run_TOPHAT.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use File::Basename; + use Cwd; + use Carp; +--- a/util/misc/run_bwa.pl ++++ b/util/misc/run_bwa.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use Cwd; + use File::Basename; + use Carp; +--- a/util/misc/run_jellyfish.pl ++++ b/util/misc/run_jellyfish.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + use Cwd; +-use FindBin; + + my $usage = "\n\nusage: $0 reads.fa hash_size\n\n"; + +@@ -11,7 +10,7 @@ my $reads_file = $ARGV[0] or die $usage; + my $hash_size = $ARGV[1] or die $usage; + + +-my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3"; ++my $JELLYFISH_DIR = "/usr"; + my $CPU = 4; + my $min_kmer_cov = 1; + +--- a/util/misc/run_read_simulator_per_gene.pl ++++ b/util/misc/run_read_simulator_per_gene.pl +@@ -5,8 +5,6 @@ use warnings; + + use lib ($ENV{EUK_MODULES}); + use Fasta_reader; +-use FindBin; +- + + my $usage = "usage: $0 file.fasta [max_genes]\n\n"; + +@@ -69,7 +67,7 @@ main: { + + my $outfile = "$sim_out_dir/$outdir/$outdir.reads.fa"; + +- my $cmd = "$FindBin::RealBin/simulate_illuminaPE_from_transcripts.pl --transcripts $template_file --SS --out_prefix $sim_out_dir/$outdir/reads"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/simulate_illuminaPE_from_transcripts.pl --transcripts $template_file --SS --out_prefix $sim_out_dir/$outdir/reads"; + &process_cmd($cmd); + + $gene_counter++; +--- a/util/misc/run_trimmomatic_qual_trimming.pl ++++ b/util/misc/run_trimmomatic_qual_trimming.pl +@@ -5,8 +5,6 @@ use warnings; + + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + +-use FindBin; +- + my $usage = <<__EOUSAGE__; + + ############################################################### +@@ -72,7 +70,7 @@ main: { + + if ($left && $right) { + +- $cmd = "java -jar $FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads $threads -phred33 " ++ $cmd = "java -jar /usr/share/java/trimmomatic.jar PE -threads $threads -phred33 " + . " $left $right " + . " $left.P.qtrim.fq $left.U.qtrim.fq " + . " $right.P.qtrim.fq $right.U.qtrim.fq " +@@ -80,7 +78,7 @@ main: { + } + else { + +- $cmd = "java -jar $FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar SE -threads $threads -phred33 " ++ $cmd = "java -jar /usr/share/java/trimmomatic.jar SE -threads $threads -phred33 " + . " $single " + . " $single.qtrim.fq " + . " $trim_params "; +--- a/util/misc/sim_test_framework/info_files_to_eval_cmds.pl ++++ b/util/misc/sim_test_framework/info_files_to_eval_cmds.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + use Cwd; +-use FindBin; + + my $usage = "usage: $0 info_files.list.txt output_basedir [eval cmds]\n\n"; + +@@ -19,7 +18,7 @@ main: { + my @files = `cat $files_listing_file`; + chomp @files; + +- my $eval_script = "$FindBin::Bin/run_Trinity_eval.sh"; ++ my $eval_script = "/usr/lib/trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.sh"; + my $basedir = cwd(); + + unless ($output_basedir =~ /^\//) { +--- a/util/misc/sim_test_framework/partition_target_transcripts.pl ++++ b/util/misc/sim_test_framework/partition_target_transcripts.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use lib ("$ENV{TRINITY_HOME}/PerlLib/"); + use Fasta_reader; + use Cwd; +--- a/util/misc/sim_test_framework/run_Trinity_eval.pl ++++ b/util/misc/sim_test_framework/run_Trinity_eval.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use lib ("$ENV{TRINITY_HOME}/PerlLib/"); + use Fasta_reader; + use Cwd; +@@ -142,7 +141,7 @@ unless ($ref_trans_fa && $BFLY_JAR && $l + $NO_CLEANUP = 1; ## NEEDED NOW for iworm and bfy pruning assessment + + unless ($ENV{TRINITY_HOME}) { +- $ENV{TRINITY_HOME} = "$FindBin::Bin/../../trinityrnaseq/"; ++ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq"; + } + + my $reconstructions_log_file = "$OUT_DIR.reconstruction_summary.txt"; +@@ -203,7 +202,7 @@ main: { + print $summary; + close $ofh; + +- &process_cmd("echo " . cwd() . "/audit.txt | $FindBin::Bin/audit_summary_stats.reexamine.pl | tee audit2.txt"); ++ &process_cmd("echo " . cwd() . "/audit.txt | /usr/lib/trinityrnaseq/util/misc/sim_test_framework/audit_summary_stats.reexamine.pl | tee audit2.txt"); + + + exit(0); +@@ -423,7 +422,7 @@ sub check_inchworm_kmer_content { + sub check_pruning { + my ($log_file, $ref_kmers_file) = @_; + +- my $pruned_ref_edges = `$FindBin::Bin/util/find_pruned_edges_shouldve_kept.pl $ref_kmers_file $log_file`; ++ my $pruned_ref_edges = `/usr/lib/trinityrnaseq/util/misc/sim_test_framework/util/find_pruned_edges_shouldve_kept.pl $ref_kmers_file $log_file`; + + if ($pruned_ref_edges =~ /\w/) { + print "Pruned precious edges: $pruned_ref_edges\n"; +--- a/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl ++++ b/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use lib ("$ENV{TRINITY_HOME}/PerlLib/"); + use Fasta_reader; + use Cwd; +@@ -95,7 +94,7 @@ unless ($ref_trans_fa && $OUT_DIR) { + + + unless ($ENV{TRINITY_HOME}) { +- $ENV{TRINITY_HOME} = "$FindBin::Bin/../../trinityrnaseq/"; ++ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq"; + } + + +--- a/util/misc/sim_test_framework/write_simulate_read_commands.pl ++++ b/util/misc/sim_test_framework/write_simulate_read_commands.pl +@@ -2,7 +2,6 @@ + + use strict; + use warnings; +-use FindBin; + use File::Basename; + + my $usage = "\n\n\tusage: $0 target_trans_files.list [opts ex. --wgsim ...]\n\n"; +@@ -18,7 +17,7 @@ main: { + + foreach my $file (@ref_files) { + my $outdir = dirname($file); +- my $cmd = "$FindBin::Bin/run_simulate_reads.wgsim.pl -R $file -O $outdir @ARGV"; ++ my $cmd = "/usr/lib/trinityrnaseq/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl -R $file -O $outdir @ARGV"; + + print "$cmd\n"; + } +--- a/util/misc/simulate_reads_sam_and_fa.pl ++++ b/util/misc/simulate_reads_sam_and_fa.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use lib "$ENV{TRINITY_HOME}/PerlLib"; + use Simulate::Uniform_Read_Generator; + use Overlap_info; +@@ -353,7 +352,7 @@ main: { + =strand_sep_trans + + if ($SS_lib_type) { +- $cmd = "$FindBin::RealBin/../support_scripts/SAM_strand_separator.pl $trans_sam_outfile.coordSorted.bam $SS_lib_type"; ++ $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl $trans_sam_outfile.coordSorted.bam $SS_lib_type"; + &process_cmd($cmd); + + foreach my $sam_file ("$trans_sam_outfile.coordSorted.bam.+.sam", "$trans_sam_outfile.coordSorted.bam.-.sam") { +@@ -398,7 +397,7 @@ main: { + =strand_sep_genome + + if ($SS_lib_type) { +- $cmd = "$FindBin::RealBin/../support_scripts/SAM_strand_separator.pl $genome_sam_outfile.coordSorted.bam $SS_lib_type"; ++ $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl $genome_sam_outfile.coordSorted.bam $SS_lib_type"; + &process_cmd($cmd); + + foreach my $sam_file ("$genome_sam_outfile.coordSorted.bam.+.sam", "$genome_sam_outfile.coordSorted.bam.-.sam") { +--- a/util/support_scripts/SAM_ordered_pair_jaccard.pl ++++ b/util/support_scripts/SAM_ordered_pair_jaccard.pl +@@ -4,7 +4,6 @@ use strict; + use warnings; + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); +-use FindBin; + + + +@@ -84,7 +83,7 @@ if (@ARGV) { + } + + +-my $util_dir = "$FindBin::RealBin"; ++my $util_dir = "/usr/lib/trinityrnaseq/util/support_scripts"; + + main: { + +--- a/util/support_scripts/bowtie2_wrapper.pl ++++ b/util/support_scripts/bowtie2_wrapper.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use Cwd; + use File::Basename; + use Carp; +@@ -11,8 +10,6 @@ use Data::Dumper; + + use Getopt::Long qw(:config no_ignore_case bundling); + +-$ENV{PATH} .= "\:$FindBin::RealBin/../trinity-plugins/rsem/sam/"; # include samtools in path, already included in rsem build. +- + $ENV{LC_ALL} = 'C'; # critical for proper sorting using [system "sort -k1,1 ..."] within the perl script + + +@@ -171,7 +168,7 @@ if ($SS_lib_type && $SS_lib_type !~ /^(F + } + + +-my $util_dir = "$FindBin::RealBin"; ++my $util_dir = "/usr/lib/trinityrnaseq/util/support_scripts"; + + my ($start_dir, $work_dir, $num_hits); + +--- a/util/support_scripts/fastQ_to_tab.pl ++++ b/util/support_scripts/fastQ_to_tab.pl +@@ -3,8 +3,6 @@ + use strict; + use warnings; + +-use FindBin; +- + use Getopt::Long qw(:config no_ignore_case bundling); + + +--- a/util/support_scripts/inchworm_transcript_splitter.pl ++++ b/util/support_scripts/inchworm_transcript_splitter.pl +@@ -5,13 +5,11 @@ use warnings; + + use Getopt::Long qw(:config no_ignore_case bundling); + +-use FindBin; +- + use Cwd; + + $ENV{LC_ALL} = 'C'; + +-my $util_dir = "$FindBin::RealBin"; ++my $util_dir = "/usr/lib/trinityrnaseq/util/support_scripts"; + + + my $usage = <<_EOUSAGE_; +--- a/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl ++++ b/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use File::Basename; + use Cwd; + +--- a/util/support_scripts/write_partitioned_trinity_cmds.pl ++++ b/util/support_scripts/write_partitioned_trinity_cmds.pl +@@ -3,7 +3,6 @@ + use strict; + use warnings; + +-use FindBin; + use Getopt::Long qw(:config no_ignore_case bundling pass_through); + + my $usage = <<__EOUSAGE__; +@@ -84,7 +83,7 @@ while (<$fh>) { + my $file = pop @x; + + +- my $cmd = "$FindBin::RealBin/../../Trinity --single \"$file\" --output \"$file.out\" $trin_args "; ++ my $cmd = "/usr/bin/Trinity --single \"$file\" --output \"$file.out\" $trin_args "; + + if ($singularity_img) { + $cmd = "singularity exec $singularity_extra_params $singularity_img $cmd"; +--- a/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py ++++ b/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py +@@ -143,7 +143,7 @@ def main(): + + args = parser.parse_args() + +- PICARD_HOME = os.getenv("PICARD_HOME") ++ PICARD_HOME = os.getenv("PICARD_HOME", "/usr/share/java") + if not PICARD_HOME: + exit("Error, missing path to Picard-Tools in $PICARD_HOME.") + +--- a/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh ++++ b/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh +@@ -20,7 +20,7 @@ find Dir_mm9chr17.tophat.* -regex ".*rea + ../../util/support_scripts/GG_write_trinity_cmds.pl --reads_list_file read_files.list --paired --SS > trinity_GG.cmds + + +-../../trinity-plugins/parafly/bin/ParaFly -c trinity_GG.cmds -CPU 2 -vv ++/usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -vv + + ## execute the trinity commands, and then pull together the aggregate fasta file like so: + find Dir_mm9chr17.tophat.* -name "*inity.fasta" | ../../util/GG_trinity_accession_incrementer.pl > mm9.Trinity-GG.fasta +--- a/util/support_scripts/trinity_install_tests.sh ++++ b/util/support_scripts/trinity_install_tests.sh +@@ -41,7 +41,7 @@ else + fi + + +-if [ -e "trinity-plugins/BIN/ParaFly" ] ++if [ -e "/usr/bin/ParaFly" ] + then + echo "parafly: has been Installed Properly" + else +--- a/Analysis/DifferentialExpression/deprecated/prep_n_run_GOplot.pl ++++ b/Analysis/DifferentialExpression/deprecated/prep_n_run_GOplot.pl +@@ -2,8 +2,7 @@ + + use strict; + use warnings; +-use FindBin; +-use lib ("$FindBin::Bin/../../PerlLib"); ++use lib ("/usr/lib/trinityrnaseq/PerlLib"); + use DelimParser; + use File::Basename; + use Data::Dumper; +@@ -144,7 +143,7 @@ main: { + } + + +- my $cmd = "$FindBin::RealBin/GOplot.Rscript --EC_david $EC_david_file --EC_genelist $EC_genelist_file --pdf_outfile $pdf_filename"; ++ my $cmd = "/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/GOplot.Rscript --EC_david $EC_david_file --EC_genelist $EC_genelist_file --pdf_outfile $pdf_filename"; + &process_cmd($cmd); + + exit(0); + diff --git a/BioArchLinux/trinityrnaseq/fix_syspath2.patch b/BioArchLinux/trinityrnaseq/fix_syspath2.patch new file mode 100644 index 0000000000..9001942bd1 --- /dev/null +++ b/BioArchLinux/trinityrnaseq/fix_syspath2.patch @@ -0,0 +1,16 @@ +Author: Michael R. Crusoe +Description: Match the Debian's path +Forwarded: not-needed +--- a/Trinity ++++ b/Trinity +@@ -56,8 +56,8 @@ if ($ENV{TRINITY_NO_RETRIES}) { + $PARAFLY .= " -max_retry 1 "; + } + +-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar"; +-my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic"; ++my $TRIMMOMATIC = "/usr/share/java/trimmomatic/trimmomatic.jar"; ++my $TRIMMOMATIC_DIR = "/usr/share/java/trimmomatic/"; + + $ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}"; + diff --git a/BioArchLinux/trinityrnaseq/lilac.yaml b/BioArchLinux/trinityrnaseq/lilac.yaml index d012100c35..84a2d40244 100644 --- a/BioArchLinux/trinityrnaseq/lilac.yaml +++ b/BioArchLinux/trinityrnaseq/lilac.yaml @@ -13,3 +13,9 @@ update_on: use_max_tag: true include_regex: Trinity-v(\d+.\d+.\d+) prefix: 'Trinity-v' +repo_depends: + - parafly + - samtools + - jellyfish + - bowtie2 + - salmon diff --git a/BioArchLinux/trinityrnaseq/list b/BioArchLinux/trinityrnaseq/list new file mode 100644 index 0000000000..5cbd7f492b --- /dev/null +++ b/BioArchLinux/trinityrnaseq/list @@ -0,0 +1,501 @@ +Analysis/DifferentialExpression/DE_graph_to_dot.pl +Analysis/DifferentialExpression/DTE_to_DTU.pl +Analysis/DifferentialExpression/GOplot.Rscript +Analysis/DifferentialExpression/Glimma.Trinity.Rscript +Analysis/DifferentialExpression/PtR +Analysis/DifferentialExpression/ROKU.pl +Analysis/DifferentialExpression/add_annot_to_trans_id.pl +Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R +Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl +Analysis/DifferentialExpression/analyze_diff_expr.pl +Analysis/DifferentialExpression/assign_tissue_specific.pl +Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl +Analysis/DifferentialExpression/cut_tree_into_clusters.pl +Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl +Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl +Analysis/DifferentialExpression/diff_express.cgi +Analysis/DifferentialExpression/downsample_count_matrix.pl +Analysis/DifferentialExpression/extract_GO_enriched_genes.pl +Analysis/DifferentialExpression/filter_diff_expr.pl +Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl +Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl +Analysis/DifferentialExpression/get_transcript_lengths.pl +Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl +Analysis/DifferentialExpression/log2_transform_matrix.pl +Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl +Analysis/DifferentialExpression/matrix_to_gene_plots.pl +Analysis/DifferentialExpression/merge_matrices.pl +Analysis/DifferentialExpression/merge_subclusters.pl +Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript +Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript +Analysis/DifferentialExpression/plot_expression_patterns.pl +Analysis/DifferentialExpression/plot_log2FC_hist.Rscript +Analysis/DifferentialExpression/prep_n_run_GOplot.pl +Analysis/DifferentialExpression/prune_isoforms_fasta.pl +Analysis/DifferentialExpression/prune_isoforms_gtf.pl +Analysis/DifferentialExpression/rank_roku_by_expr.pl +Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl +Analysis/DifferentialExpression/rename_matrix_column_labels.pl +Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl +Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl +Analysis/DifferentialExpression/run_DE_analysis.pl +Analysis/DifferentialExpression/run_GOseq.pl +Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl +Analysis/DifferentialExpression/stratify_diff_expression.pl +Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl +Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl +Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl +Analysis/DifferentialExpression/validate_UP_subset.Rscript +Analysis/DifferentialExpression/R/edgeR.TMM.minimal.R +Analysis/DifferentialExpression/R/edgeR_funcs.R +Analysis/DifferentialExpression/R/get_cluster_info.R +Analysis/DifferentialExpression/R/heatmap.3.R +Analysis/DifferentialExpression/R/jaccard_distance.R +Analysis/DifferentialExpression/R/manually_define_clusters.R +Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R +Analysis/DifferentialExpression/R/pairs3.R +Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R +Analysis/DifferentialExpression/R/test.heatmap.3.R +Analysis/DifferentialExpression/R/vioplot2.R +Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R +Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl +Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl +Analysis/DifferentialExpression/TissueEnrichment/README.md +Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl +Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl +Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz +Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl +Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt +Analysis/DifferentialExpression/cluster_sample_data/runMe.sh +Analysis/DifferentialExpression/cluster_sample_data/samples.txt +Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix +Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl +Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl +Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl +Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl +Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl +Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl +Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl +Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl +Analysis/DifferentialExpression/pairwise_summaries/notes +Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl +Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl +Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl +Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl +Analysis/FL_reconstruction_analysis/compute_oracle.pl +Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl +Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl +Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl +Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl +Analysis/FL_reconstruction_analysis/oracle_counter.pl +Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl +Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl +Analysis/FL_reconstruction_analysis/R/boot.tree.R +Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl +Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl +Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl +Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl +Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl +Analysis/SuperTranscripts/README.md +Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py +Analysis/SuperTranscripts/extract_supertranscript_from_reference.py +Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl +Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py +Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl +Analysis/SuperTranscripts/DTU/README.md +Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl +Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl +Analysis/SuperTranscripts/_misc/aln_before_after.pl +Analysis/SuperTranscripts/pylib/Compact_graph_partial.py +Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py +Analysis/SuperTranscripts/pylib/Compact_graph_whole.py +Analysis/SuperTranscripts/pylib/DP_matrix.py +Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py +Analysis/SuperTranscripts/pylib/GraphCycleException.py +Analysis/SuperTranscripts/pylib/Node_alignment.py +Analysis/SuperTranscripts/pylib/Node_path.py +Analysis/SuperTranscripts/pylib/Splice_model_refiner.py +Analysis/SuperTranscripts/pylib/TGLOBALS.py +Analysis/SuperTranscripts/pylib/TGraph.py +Analysis/SuperTranscripts/pylib/TNode.py +Analysis/SuperTranscripts/pylib/Topological_sort.py +Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py +Analysis/SuperTranscripts/pylib/Trinity_util.py +Analysis/SuperTranscripts/pylib/__init__.py +PerlLib/Ascii_genome_illustrator.pm +PerlLib/BED_utils.pm +PerlLib/BHStats.pm +PerlLib/CIGAR.pm +PerlLib/CMD_processor.pm +PerlLib/COMMON.pm +PerlLib/ColorGradient.pm +PerlLib/DelimParser.pm +PerlLib/EM.pm +PerlLib/Exons_to_geneobj.pm +PerlLib/Fasta_reader.pm +PerlLib/Fasta_retriever.pm +PerlLib/Fastq_reader.pm +PerlLib/GFF3_alignment_utils.pm +PerlLib/GFF3_utils.pm +PerlLib/GFF_maker.pm +PerlLib/GTF.pm +PerlLib/GTF_utils.pm +PerlLib/Gene_obj.pm +PerlLib/Gene_obj_indexer.pm +PerlLib/Ktree.pm +PerlLib/Longest_orf.pm +PerlLib/Nuc_translator.pm +PerlLib/Overlap_info.pm +PerlLib/Overlap_piler.pm +PerlLib/PSL_parser.pm +PerlLib/Pipeliner.pm +PerlLib/Process_cmd.pm +PerlLib/SAM_entry.pm +PerlLib/SAM_reader.pm +PerlLib/SingleLinkageClusterer.pm +PerlLib/Thread_helper.pm +PerlLib/TiedHash.pm +PerlLib/VCF_parser.pm +PerlLib/WigParser.pm +PerlLib/overlapping_nucs.ph +PerlLib/test_Fasta_retriever.pl +PerlLib/test_htc_gridrunner_LSF.pl +PerlLib/test_htc_gridrunner_SGE.pl +PerlLib/CDNA/Alignment_segment.pm +PerlLib/CDNA/Alternative_splice_comparer.pm +PerlLib/CDNA/CDNA_alignment.pm +PerlLib/CDNA/CDNA_stitcher.pm +PerlLib/CDNA/Gene_obj_alignment_assembler.pm +PerlLib/CDNA/Genome_based_cDNA_assembler.pm +PerlLib/CDNA/Genome_based_cDNA_graph_assembler.pm +PerlLib/CDNA/Overlap_assembler.pm +PerlLib/CDNA/PASA_alignment_assembler.pm +PerlLib/CDNA/Splice_graph_assembler.pm +PerlLib/CanvasXpress/Heatmap.pm +PerlLib/KmerGraphLib/AlignGraph.pm +PerlLib/KmerGraphLib/AlignNode.pm +PerlLib/KmerGraphLib/GenericGraph.pm +PerlLib/KmerGraphLib/GenericNode.pm +PerlLib/KmerGraphLib/KmerGraph.pm +PerlLib/KmerGraphLib/KmerNode.pm +PerlLib/KmerGraphLib/ReadCoverageGraph.pm +PerlLib/KmerGraphLib/ReadCoverageNode.pm +PerlLib/KmerGraphLib/ReadManager.pm +PerlLib/KmerGraphLib/ReadTracker.pm +PerlLib/KmerGraphLib/SAM_entry.pm +PerlLib/KmerGraphLib/SAM_reader.pm +PerlLib/KmerGraphLib/SAM_to_AlignGraph.pm 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+util/PBS/trinity_pbs.cont +util/PBS/trinity_pbs.header +util/PBS/trinity_pbs.p1 +util/PBS/trinity_pbs.p2 +util/PBS/trinity_pbs.p3 +util/PBS/trinity_pbs.p4a +util/PBS/trinity_pbs.p4b +util/PBS/trinity_pbs.p5b +util/PBS/trinity_pbs.sh +util/R/expression_analysis_lib.R +util/R/get_Poisson_conf_intervals.R +util/misc/ButterflyFastaToGraphDot.pl +util/misc/HiCpipe_nameSortedSam_to_raw.pl +util/misc/Monarch +util/misc/N50.pl +util/misc/SAM_coordsorted_max_reads_per_position.pl +util/misc/SAM_intron_extractor.pl +util/misc/SAM_nameSorted_to_uniq_count_stats.pl +util/misc/SAM_pair_to_bed.pl +util/misc/SAM_show_alignment.pl +util/misc/SAM_show_alignment.summarize_stats.pl +util/misc/SAM_sortAny_to_count_stats.pl +util/misc/SAM_toString.pl +util/misc/SAM_to_bed.pl +util/misc/SAM_to_fasta.pl +util/misc/SRA_to_fastq.notes +util/misc/SRA_to_fastq.pl +util/misc/TPM_weighted_gene_length.py +util/misc/TophatCufflinksWrapper.pl +util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl +util/misc/acc_list_to_fasta_entries.pl +util/misc/alexie_analyze_blast.pl +util/misc/align_reads_launch_igv.pl +util/misc/allele_simulator.pl +util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl +util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl +util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl +util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl +util/misc/average.pl +util/misc/blast_outfmt6_group_segments.pl +util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl +util/misc/blast_outfmt6_group_segments.tophit_coverage.pl +util/misc/blastn_wrapper.pl +util/misc/capture_orig_n_unmapped_reads.pl +util/misc/cat_require_newlines.pl +util/misc/cdhit_examine_isoforms.pl +util/misc/cdna_fasta_file_to_transcript_gtf.pl +util/misc/check_chrysalis_graph_reciprocal_edges.pl +util/misc/check_fastQ_pair_ordering.pl +util/misc/chrys_graph_to_dot.pl +util/misc/collate_fqs.pl +util/misc/combined_nameSorted_to_dup_pairs_removed.pl +util/misc/compare_FL_stats.pl +util/misc/compare_bflies.pl +util/misc/component_to_graph_dot.pl +util/misc/contig_ExN50_statistic.pl +util/misc/convert_fasta_identifiers_for_FL_analysis.pl +util/misc/count_N50_given_MIN_FPKM_threshold.pl +util/misc/count_features_given_MIN_FPKM_threshold.pl +util/misc/count_iso_per_gene_dist.pl +util/misc/count_matrix_features_given_MIN_TPM_threshold.pl +util/misc/count_number_fasta_seqs.pl +util/misc/count_trans_per_component.pl +util/misc/decode_SAM_flag_value.pl +util/misc/describe_SAM_read_flag_info.pl +util/misc/determine_RF_strand_specificity.pl +util/misc/ensure_paired_end_bam_file.pl +util/misc/examine_iworm_FL_across_threads.pl +util/misc/examine_strand_specificity.pl +util/misc/examine_weldmer_halves.pl +util/misc/extract_fastQ_pairings.pl +util/misc/fan_out_fasta_seqs_to_indiv_files.pl +util/misc/fastQ_append_acc.pl +util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl +util/misc/fastQ_rand_subset.pl +util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl +util/misc/fastQ_top_N_records.pl +util/misc/fasta_file_reformatter.pl +util/misc/fasta_filter_by_min_length.pl +util/misc/fasta_remove_duplicates.pl +util/misc/fasta_seq_length.pl +util/misc/fasta_to_cmd_generator.pl +util/misc/fasta_write_sense_n_anti.pl +util/misc/fastq_cleaner.pl +util/misc/fastq_interleave_pairs.pl +util/misc/fastq_merge_sorted_tab_lists.pl +util/misc/fastq_stats.pl +util/misc/fastq_unweave_pairs.pl +util/misc/filter_out_accs_from_fasta.pl +util/misc/filter_similar_seqs_expr_and_strand_aware.pl +util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl +util/misc/frag_boundary_to_wig.pl +util/misc/frag_to_bed.pl +util/misc/gene_gff3_to_introns.pl +util/misc/gene_to_shared_transcript_content.pl +util/misc/genome_gff3_to_gene_gff3_partitions.pl +util/misc/get_GC_content_dist.pl +util/misc/get_longest_isoform_seq_per_trinity_gene.pl +util/misc/get_path_nodes_from_fasta.pl +util/misc/get_welds_from_chrysals_graphFromFasta_out.pl +util/misc/gff3_file_to_cdna.pl +util/misc/gff3_file_utr_coverage_trimmer.pl +util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl +util/misc/gff3_to_genome_feature_base_encoding.pl +util/misc/gmap_gff3_chimera_jaccard_analyzer.pl +util/misc/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl +util/misc/gmap_gff3_to_percent_length_stats.pl +util/misc/gmap_native_to_format_converter.pl +util/misc/gtf_to_bed_format.pl +util/misc/gtf_to_introns.pl +util/misc/hicpipe_raw_converter.pl +util/misc/identify_distal_isoform_variations.pl +util/misc/illustrate_ref_comparison.pl +util/misc/iworm_welds_to_dot.pl +util/misc/jaccard_sam_pair_refiner.pl +util/misc/join_any.pl +util/misc/join_by_left_col.pl +util/misc/join_expr_vals_single_table.pl +util/misc/kmer_counter.pl +util/misc/m8_blastclust.pl +util/misc/map_gtf_transcripts_to_genome_annots.pl +util/misc/merge_RSEM_output_to_matrix.pl +util/misc/merge_blast_n_rsem_results.pl +util/misc/merge_rsem_n_express_for_compare.pl +util/misc/mpi_iworm_proc_contigs_to_fa.pl +util/misc/nameSorted_SAM_to_FastQ.pl +util/misc/nameSorted_SAM_to_paired_fastq.pl +util/misc/omp_iworm_thread_contigs_to_fa.pl +util/misc/organize_data_table_by_trinity_component.pl +util/misc/pair_up_fastq_files_1_2.pl +util/misc/pair_up_fastq_files_LeftRight.pl +util/misc/pair_up_fastq_files_R1_R2.pl +util/misc/pairwise_kmer_content_comparer.pl +util/misc/plot_ExN50_statistic.Rscript +util/misc/plot_expressed_gene_dist.pl +util/misc/plot_strand_specificity_dist_by_quantile.Rscript +util/misc/print.pl +util/misc/print_kmers.pl +util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl +util/misc/prop_pair_sam_refiner.pl +util/misc/randomly_mutate_seqs.pl +util/misc/randomly_sample_PE_fastq.pl +util/misc/remove_cntrl_chars.pl +util/misc/row_to_column.pl +util/misc/run_DETONATE.pl +util/misc/run_GSNAP.pl +util/misc/run_HISAT.pl +util/misc/run_HISAT2_via_samples_file.pl +util/misc/run_HiCpipe_bowtie.pl +util/misc/run_STAR.pl +util/misc/run_STAR_via_samples_file.pl +util/misc/run_TOPHAT.pl +util/misc/run_bowtie2.pl +util/misc/run_bwa.pl +util/misc/run_bwasw_trinity.pl +util/misc/run_jellyfish.pl +util/misc/run_read_simulator_per_fasta_entry.pl +util/misc/run_read_simulator_per_gene.pl +util/misc/run_trimmomatic_qual_trimming.pl +util/misc/seqinfo_refseq_to_dot.pl +util/misc/shuffle.pl +util/misc/simulate_illuminaPE_from_transcripts.pl +util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl +util/misc/simulate_reads_sam_and_fa.pl +util/misc/sixFrameTranslation.pl +util/misc/sort_fastq.pl +util/misc/strip_fasta_header.pl +util/misc/tab_to_fastQ.pl +util/misc/tab_to_fasta.pl +util/misc/tblastn_wrapper.pl +util/misc/testUnlimitStacksize.pl +util/misc/transcript_coverage_UTR_trimmer.pl +util/misc/transcript_fasta_to_ORF_pics.pl +util/misc/transcript_gff3_to_bed.pl +util/misc/transdecoder_pep_to_false_fusion_finder.pl +util/misc/trinity_component_distribution.pl +util/misc/trinity_trans_matrix_to_rep_trans_gene_matrix.pl +util/misc/Artemis/join_multi_wig_to_graph_plot.pl +util/misc/Monarch_util/generate_gene_alt_splicing_graphs.pl +util/misc/Monarch_util/generate_trans_graphs.pl +util/misc/PerlLib/SegmentGraph.pm +util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl +util/misc/alt_GG_read_partitioning_JCornish/genwig.sh +util/misc/alt_GG_read_partitioning_JCornish/genwig2.py +util/misc/altsplice_simulation_toolkit/sim_single_bubble.pl +util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl +util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl +util/misc/bam_gene_tests/harvest_transcripts.pl +util/misc/bam_gene_tests/write_trin_cmds.pl +util/misc/blat_util/blat_sam_add_reads2.pl +util/misc/blat_util/blat_to_sam.pl +util/misc/blat_util/blat_top_hit_extractor.pl +util/misc/blat_util/process_BLAT_alignments.pl +util/misc/blat_util/pslx_to_gff3.pl +util/misc/blat_util/run_BLAT_shortReads.pl +util/misc/blat_util/top_blat_sam_extractor.pl +util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt +util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt +util/misc/insilico_norm_kmer_hists/plot_me.R +util/misc/insilico_norm_kmer_hists/result.pdf +util/misc/iso_reco_analysis/bam_to_cuff.pl +util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl +util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl +util/misc/iso_reco_analysis/gmap_to_ref.pl +util/misc/iso_reco_analysis/notes +util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl +util/misc/iso_reco_analysis/run_trinity_no_LR.pl +util/misc/iso_reco_analysis/sim_reads.pl +util/misc/iso_reco_analysis/trans_gff3_to_bed_cmds.pl +util/misc/sim_test_framework/audit_summary_stats.pl +util/misc/sim_test_framework/audit_summary_stats.reexamine.pl +util/misc/sim_test_framework/info_files_to_eval_cmds.pl +util/misc/sim_test_framework/partition_target_transcripts.pl +util/misc/sim_test_framework/run_Trinity_eval.pl +util/misc/sim_test_framework/run_Trinity_eval.sh +util/misc/sim_test_framework/run_simulate_reads.wgsim.pl +util/misc/sim_test_framework/write_simulate_read_commands.pl +util/misc/sim_test_framework/util/find_pruned_edges_shouldve_kept.pl +util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl +util/misc/splice_path_analysis/assess_intron_path_sensitivity.summarizer.pl +util/misc/splice_path_analysis/diff_splice_paths.pl +util/misc/splice_path_analysis/intron_barcharter.pl +util/support_scripts/GG_partitioned_trinity_aggregator.pl +util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl +util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl +util/support_scripts/SAM_extract_properly_mapped_pairs.pl +util/support_scripts/SAM_extract_uniquely_mapped_reads.pl +util/support_scripts/SAM_filter_out_unmapped_reads.pl +util/support_scripts/SAM_ordered_pair_jaccard.pl +util/support_scripts/SAM_set_transcribed_orient_info.pl +util/support_scripts/SAM_strand_separator.pl +util/support_scripts/SAM_to_frag_coords.pl +util/support_scripts/add_LR_reads_to_iworm_bundle.pl +util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl +util/support_scripts/batch_cmds.pl +util/support_scripts/bowtie2_wrapper.pl +util/support_scripts/define_SAM_coverage_partitions2.pl +util/support_scripts/define_coverage_partitions.pl +util/support_scripts/eXpress_trans_to_gene_results.pl +util/support_scripts/ensure_coord_sorted_sam.pl +util/support_scripts/extract_reads_per_partition.pl +util/support_scripts/fastQ_to_fastA.pl +util/support_scripts/fastQ_to_tab.pl +util/support_scripts/fasta_find_duplicates.pl +util/support_scripts/fasta_to_tab.pl +util/support_scripts/filter_iworm_by_min_length_or_cov.pl +util/support_scripts/filter_transcripts_require_min_cov.pl +util/support_scripts/fragment_coverage_writer.pl +util/support_scripts/get_Trinity_gene_to_trans_map.pl +util/support_scripts/inchworm_transcript_splitter.pl +util/support_scripts/iworm_LR_to_scaff_pairs.pl +util/support_scripts/jaccard_fasta_clipper.pl +util/support_scripts/jaccard_wig_clipper.pl +util/support_scripts/join_partitions_within_range.pl +util/support_scripts/kallisto_trans_to_gene_results.pl +util/support_scripts/merge_pair_and_LR_scaff_links.pl +util/support_scripts/nbkc_merge_left_right_stats.pl +util/support_scripts/nbkc_normalize.pl +util/support_scripts/ordered_fragment_coords_to_jaccard.pl +util/support_scripts/outfmt6_add_percent_match_length.pl +util/support_scripts/partition_chrysalis_graphs_n_reads.pl +util/support_scripts/partitioned_trinity_aggregator.pl +util/support_scripts/plugin_install_tests.sh +util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl +util/support_scripts/print_butterfly_assemblies.pl +util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl +util/support_scripts/revcomp_fasta.pl +util/support_scripts/run_TMM_scale_matrix.pl +util/support_scripts/run_UpperQuartileNormalization_matrix.pl +util/support_scripts/salmon_runner.pl +util/support_scripts/salmon_trans_to_gene_results.pl +util/support_scripts/scaffold_iworm_contigs.pl +util/support_scripts/segment_GFF_partitions.pl +util/support_scripts/trinity_install_tests.sh +util/support_scripts/trinity_installer.py +util/support_scripts/wig_clip_to_bed.pl +util/support_scripts/write_partitioned_trinity_cmds.pl +util/support_scripts/tests/sample_data_tests.py +util/support_scripts/tests/test_prep.py +util/support_scripts/tests/tests.py +usr/share/doc/trinityrnaseq/README +usr/share/doc/trinityrnaseq/TODO.Debian +usr/share/doc/trinityrnaseq/changelog.Debian.gz +usr/share/doc/trinityrnaseq/changelog.gz +usr/share/doc/trinityrnaseq/copyright +usr/share/doc/trinityrnaseq/run-tests +usr/share/java/Butterfly-2.11.0.jar +usr/share/man/man1/Trinity.1.gz diff --git a/BioArchLinux/trinityrnaseq/string.patch b/BioArchLinux/trinityrnaseq/string.patch deleted file mode 100644 index 8647aad3ac..0000000000 --- a/BioArchLinux/trinityrnaseq/string.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp -index e8ecbcf..ccdbd27 100644 ---- a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp -+++ b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp -@@ -10,6 +10,7 @@ - #include - #include - #include -+#include - - #include "htslib/sam.h" - #include "htslib/bgzf.h"