From 173e741447ec7bb0e6e814b4169eaa6d4e78ea6b Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Mon, 3 Jan 2022 18:53:02 +0100 Subject: [PATCH 01/10] Add lra --- BioArchLinux/lra/PKGBUILD | 26 ++++++++++++++++++++++++++ BioArchLinux/lra/lilac.py | 11 +++++++++++ BioArchLinux/lra/lilac.yaml | 9 +++++++++ 3 files changed, 46 insertions(+) create mode 100644 BioArchLinux/lra/PKGBUILD create mode 100644 BioArchLinux/lra/lilac.py create mode 100644 BioArchLinux/lra/lilac.yaml diff --git a/BioArchLinux/lra/PKGBUILD b/BioArchLinux/lra/PKGBUILD new file mode 100644 index 0000000000..6eb16359b7 --- /dev/null +++ b/BioArchLinux/lra/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Mick Elliot +# Contributor: Mick Elliot + +pkgname=lra +pkgver=1.3.2 +pkgrel=1 +pkgdesc='A long read aligner for sequences and contigs. doi:10.1371/journal.pcbi.1009078' +arch=('x86_64') +url="https://github.com/ChaissonLab/${pkgname^^}" +license=('USC-RL v1.0') +depends=('zlib' 'htslib') +provides=('lra') +source=("${pkgver}.tar.gz::${url}/archive/refs/tags/${pkgver}.tar.gz") +sha256sums=('a0ec18d4bd2bc196eb4063ad45fcdb306f212feddca6a7aca8ef87122a0cca1f') + +build() { + cd "${pkgname^^}-${pkgver}" + make +} + +package() { + cd "${pkgname^^}-${pkgver}" + install -Dm644 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE" + install -Dm644 lra "${pkgdir}/usr/bin/${pkgname}" + chmod +x "${pkgdir}/usr/bin/${pkgname}" +} diff --git a/BioArchLinux/lra/lilac.py b/BioArchLinux/lra/lilac.py new file mode 100644 index 0000000000..e3ec09df9a --- /dev/null +++ b/BioArchLinux/lra/lilac.py @@ -0,0 +1,11 @@ +#!/usr/bin/env python3 + +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() + diff --git a/BioArchLinux/lra/lilac.yaml b/BioArchLinux/lra/lilac.yaml new file mode 100644 index 0000000000..b38ada0384 --- /dev/null +++ b/BioArchLinux/lra/lilac.yaml @@ -0,0 +1,9 @@ +build_prefix: extra-x86_64 +maintainers: + - github: michaelgelliot + email: m.g.elliot@rug.nl +update_on: + - source: github + github: ChaissonLab/LRA + use_max_tag: true + From ec409cf44da049db964401bed9e5aa63d80a6458 Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Mon, 3 Jan 2022 20:03:02 +0100 Subject: [PATCH 02/10] Add GSAlign, fix pkgbuild for lra --- BioArchLinux/gsalign/PKGBUILD | 29 +++++++++++++++++++++++++++++ BioArchLinux/gsalign/lilac.py | 12 ++++++++++++ BioArchLinux/gsalign/lilac.yaml | 10 ++++++++++ BioArchLinux/lra/PKGBUILD | 2 +- 4 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 BioArchLinux/gsalign/PKGBUILD create mode 100644 BioArchLinux/gsalign/lilac.py create mode 100644 BioArchLinux/gsalign/lilac.yaml diff --git a/BioArchLinux/gsalign/PKGBUILD b/BioArchLinux/gsalign/PKGBUILD new file mode 100644 index 0000000000..eceeb3a267 --- /dev/null +++ b/BioArchLinux/gsalign/PKGBUILD @@ -0,0 +1,29 @@ +# Maintainer: Mick Elliot +# Contributor: Mick Elliot + +pkgname=gsalign +pkgnamecaps=GSAlign +pkgver=1.0.22 +pkgrel=1 +pkgdesc='An ultra-fast sequence alignment algorithm for intra-species genome comparison. doi:10.1186/s12864-020-6569-1' +arch=('x86_64') +url="https://github.com/hsinnan75/${pkgnamecaps}" +license=('MIT') +depends=(gcc-libs zlib) +provides=() +source=("${pkgver}.tar.gz::${url}/archive/refs/tags/${pkgver}.tar.gz") +sha256sums=('832eb3f570756cf6c0165036994a184e8882b152f3163d50367caa9d0815f619') + +build() { + cd "${pkgnamecaps}-${pkgver}" + make +} + +package() { + cd "${pkgnamecaps}-${pkgver}" + install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE" + install -Dm644 bin/bwt_index "${pkgdir}/usr/bin/bwt_index" + install -Dm644 bin/${pkgnamecaps} "${pkgdir}/usr/bin/${pkgnamecaps}" + chmod +x "${pkgdir}/usr/bin/bwt_index" + chmod +x "${pkgdir}/usr/bin/${pkgnamecaps}" +} diff --git a/BioArchLinux/gsalign/lilac.py b/BioArchLinux/gsalign/lilac.py new file mode 100644 index 0000000000..e397926cc8 --- /dev/null +++ b/BioArchLinux/gsalign/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 + +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() + + diff --git a/BioArchLinux/gsalign/lilac.yaml b/BioArchLinux/gsalign/lilac.yaml new file mode 100644 index 0000000000..6b0d22e0de --- /dev/null +++ b/BioArchLinux/gsalign/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: + - github: michaelgelliot + email: m.g.elliot@rug.nl +update_on: + - source: github + github: hsinnan75/GSAlign + use_max_tag: true + + diff --git a/BioArchLinux/lra/PKGBUILD b/BioArchLinux/lra/PKGBUILD index 6eb16359b7..e44aec8f7f 100644 --- a/BioArchLinux/lra/PKGBUILD +++ b/BioArchLinux/lra/PKGBUILD @@ -9,7 +9,7 @@ arch=('x86_64') url="https://github.com/ChaissonLab/${pkgname^^}" license=('USC-RL v1.0') depends=('zlib' 'htslib') -provides=('lra') +provides=('') source=("${pkgver}.tar.gz::${url}/archive/refs/tags/${pkgver}.tar.gz") sha256sums=('a0ec18d4bd2bc196eb4063ad45fcdb306f212feddca6a7aca8ef87122a0cca1f') From 7c08e3c140f5555f0a459435ce80d077d033259a Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Mon, 3 Jan 2022 20:36:41 +0100 Subject: [PATCH 03/10] Add minimap2, correct pkgbuild for lra --- BioArchLinux/lra/PKGBUILD | 2 +- BioArchLinux/minimap2/PKGBUILD | 25 +++++++++++++++++++++++++ BioArchLinux/minimap2/lilac.py | 11 +++++++++++ BioArchLinux/minimap2/lilac.yaml | 10 ++++++++++ 4 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 BioArchLinux/minimap2/PKGBUILD create mode 100644 BioArchLinux/minimap2/lilac.py create mode 100644 BioArchLinux/minimap2/lilac.yaml diff --git a/BioArchLinux/lra/PKGBUILD b/BioArchLinux/lra/PKGBUILD index e44aec8f7f..fc843bc00e 100644 --- a/BioArchLinux/lra/PKGBUILD +++ b/BioArchLinux/lra/PKGBUILD @@ -9,7 +9,7 @@ arch=('x86_64') url="https://github.com/ChaissonLab/${pkgname^^}" license=('USC-RL v1.0') depends=('zlib' 'htslib') -provides=('') +provides=() source=("${pkgver}.tar.gz::${url}/archive/refs/tags/${pkgver}.tar.gz") sha256sums=('a0ec18d4bd2bc196eb4063ad45fcdb306f212feddca6a7aca8ef87122a0cca1f') diff --git a/BioArchLinux/minimap2/PKGBUILD b/BioArchLinux/minimap2/PKGBUILD new file mode 100644 index 0000000000..e5d4af08f7 --- /dev/null +++ b/BioArchLinux/minimap2/PKGBUILD @@ -0,0 +1,25 @@ +# Maintainer: Mick Elliot +# Contributor: Mick Elliot + +pkgname=minimap2 +pkgver=2.24 +pkgrel=1 +pkgdesc='A versatile pairwise aligner for genomic and spliced nucleotide sequences. doi:10.1093/bioinformatics/bty191' +arch=('x86_64') +url="https://github.com/lh3/${pkgname}" +license=('MIT') +depends=(zlib) +provides=() +source=("${pkgver}.tar.gz::${url}/releases/download/v${pkgver}/${pkgname}-${pkgver}.tar.bz2") +sha256sums=('9dd4c31ff082182948944bcdad6d328f64f09295d10547d72eba24189880a615') +build() { + cd "${pkgname}-${pkgver}" + make +} + +package() { + cd "${pkgname}-${pkgver}" + install -Dm644 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE" + install -Dm644 ${pkgname} "${pkgdir}/usr/bin/${pkgname}" + chmod +x "${pkgdir}/usr/bin/${pkgname}" +} diff --git a/BioArchLinux/minimap2/lilac.py b/BioArchLinux/minimap2/lilac.py new file mode 100644 index 0000000000..e3ec09df9a --- /dev/null +++ b/BioArchLinux/minimap2/lilac.py @@ -0,0 +1,11 @@ +#!/usr/bin/env python3 + +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() + diff --git a/BioArchLinux/minimap2/lilac.yaml b/BioArchLinux/minimap2/lilac.yaml new file mode 100644 index 0000000000..edb5783c81 --- /dev/null +++ b/BioArchLinux/minimap2/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: + - github: michaelgelliot + email: m.g.elliot@rug.nl +update_on: + - source: github + github: lh3/minimap2 + use_max_tag: true + + From 30d5a9ce9add3765b7ffec6139c9b4e307059e51 Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Mon, 3 Jan 2022 23:02:27 +0100 Subject: [PATCH 04/10] Added a DOI to the pkgdesc of most PKGBUILD files --- BioArchLinux/avogadro2/PKGBUILD | 2 +- BioArchLinux/bali-phy/PKGBUILD | 2 +- BioArchLinux/beast/PKGBUILD | 2 +- BioArchLinux/beast2/PKGBUILD | 2 +- BioArchLinux/blast+/PKGBUILD | 2 +- BioArchLinux/bowtie/PKGBUILD | 2 +- BioArchLinux/bowtie2/PKGBUILD | 2 +- BioArchLinux/bwa/PKGBUILD | 2 +- BioArchLinux/clustal-omega/PKGBUILD | 2 +- BioArchLinux/clustalw/PKGBUILD | 2 +- BioArchLinux/clustalx/PKGBUILD | 2 +- BioArchLinux/easycodeml/PKGBUILD | 2 +- BioArchLinux/emboss/PKGBUILD | 2 +- BioArchLinux/fasttree/PKGBUILD | 2 +- BioArchLinux/fastx-toolkit/PKGBUILD | 2 +- BioArchLinux/gblocks/PKGBUILD | 2 +- BioArchLinux/hmmer/PKGBUILD | 2 +- BioArchLinux/htslib/PKGBUILD | 2 +- BioArchLinux/insight-toolkit/PKGBUILD | 2 +- BioArchLinux/iqtree/PKGBUILD | 2 +- BioArchLinux/jane/PKGBUILD | 2 +- BioArchLinux/jmodeltest/PKGBUILD | 2 +- BioArchLinux/mafft/PKGBUILD | 2 +- BioArchLinux/mega/PKGBUILD | 2 +- BioArchLinux/modeltest-ng/PKGBUILD | 2 +- BioArchLinux/morphoj/PKGBUILD | 2 +- BioArchLinux/mrbayes-mpi/PKGBUILD | 2 +- BioArchLinux/mrbayes/PKGBUILD | 2 +- BioArchLinux/muscle/PKGBUILD | 2 +- BioArchLinux/paml/PKGBUILD | 2 +- BioArchLinux/paup/PKGBUILD | 2 +- BioArchLinux/phylip/PKGBUILD | 2 +- BioArchLinux/phylobayes-mpi/PKGBUILD | 2 +- BioArchLinux/phylobayes/PKGBUILD | 2 +- BioArchLinux/phylonet-hmm/PKGBUILD | 2 +- BioArchLinux/phylonet/PKGBUILD | 2 +- BioArchLinux/phylonium/PKGBUILD | 2 +- BioArchLinux/phylosuite/PKGBUILD | 2 +- BioArchLinux/phyml/PKGBUILD | 2 +- BioArchLinux/pibuss/PKGBUILD | 2 +- BioArchLinux/popart/PKGBUILD | 2 +- BioArchLinux/primer3/PKGBUILD | 2 +- BioArchLinux/rasp/PKGBUILD | 2 +- BioArchLinux/raxml-mpi/PKGBUILD | 2 +- BioArchLinux/raxml-ng-mpi/PKGBUILD | 2 +- BioArchLinux/raxml-ng/PKGBUILD | 2 +- BioArchLinux/raxml/PKGBUILD | 2 +- BioArchLinux/raxmlgui/PKGBUILD | 2 +- BioArchLinux/samtools/PKGBUILD | 2 +- BioArchLinux/seaview/PKGBUILD | 2 +- BioArchLinux/seqan/PKGBUILD | 2 +- BioArchLinux/seqan3/PKGBUILD | 2 +- BioArchLinux/spread/PKGBUILD | 2 +- BioArchLinux/spread3/PKGBUILD | 2 +- BioArchLinux/tempest/PKGBUILD | 2 +- BioArchLinux/tiger/PKGBUILD | 2 +- BioArchLinux/tnt-gui/PKGBUILD | 2 +- BioArchLinux/tnt-mpi/PKGBUILD | 2 +- BioArchLinux/tnt/PKGBUILD | 2 +- BioArchLinux/tracer/PKGBUILD | 2 +- BioArchLinux/tracy/PKGBUILD | 2 +- BioArchLinux/trimal/PKGBUILD | 2 +- BioArchLinux/ugene/PKGBUILD | 2 +- BioArchLinux/vcftools/PKGBUILD | 2 +- 64 files changed, 64 insertions(+), 64 deletions(-) diff --git a/BioArchLinux/avogadro2/PKGBUILD b/BioArchLinux/avogadro2/PKGBUILD index cd43263a55..542c8d62bb 100644 --- a/BioArchLinux/avogadro2/PKGBUILD +++ b/BioArchLinux/avogadro2/PKGBUILD @@ -5,7 +5,7 @@ pkgname=avogadro2 _pkgname=avogadroapp pkgver=1.95.1 pkgrel=5 -pkgdesc="An advanced molecular editor" +pkgdesc="An advanced molecular editor. doi:10.1186/1758-2946-4-17" arch=('x86_64') url="https://two.avogadro.cc" license=('BSD') diff --git a/BioArchLinux/bali-phy/PKGBUILD b/BioArchLinux/bali-phy/PKGBUILD index f6b6b618a3..d98d8fdf55 100644 --- a/BioArchLinux/bali-phy/PKGBUILD +++ b/BioArchLinux/bali-phy/PKGBUILD @@ -2,7 +2,7 @@ pkgname=bali-phy pkgver=3.6.1 pkgrel=4 -pkgdesc="Bayesian co-estimation of phylogenies and multiple alignments via MCMC" +pkgdesc="Bayesian co-estimation of phylogenies and multiple alignments via MCMC. doi:10.1093/bioinformatics/btab129" arch=('x86_64') url="http://www.bali-phy.org/" license=('GPL') diff --git a/BioArchLinux/beast/PKGBUILD b/BioArchLinux/beast/PKGBUILD index f2bba4742c..0c562ede1d 100644 --- a/BioArchLinux/beast/PKGBUILD +++ b/BioArchLinux/beast/PKGBUILD @@ -5,7 +5,7 @@ pkgname=beast pkgver=1.10.4 pkgrel=8 provides=("beast") -pkgdesc="Bayesian Evolutionary Analysis Sampling Trees" +pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. doi:10.1186/1471-2148-7-214" arch=('x86_64') url="http://beast.community/" license=('LGPL-2.1 License') diff --git a/BioArchLinux/beast2/PKGBUILD b/BioArchLinux/beast2/PKGBUILD index e406be7661..0605526843 100644 --- a/BioArchLinux/beast2/PKGBUILD +++ b/BioArchLinux/beast2/PKGBUILD @@ -4,7 +4,7 @@ pkgname=beast2 pkgver=2.6.6 pkgrel=3 -pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees" +pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. 10.1371/journal.pcbi.1003537" arch=('x86_64') url="http://www.beast2.org/" license=('LGPL-2.1 License') diff --git a/BioArchLinux/blast+/PKGBUILD b/BioArchLinux/blast+/PKGBUILD index bc02a01632..ec30032d49 100755 --- a/BioArchLinux/blast+/PKGBUILD +++ b/BioArchLinux/blast+/PKGBUILD @@ -5,7 +5,7 @@ pkgname=blast+ pkgver=2.12.0 pkgrel=4 -pkgdesc='BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc)' +pkgdesc='BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc). doi:10.1186/1471-2105-10-421' arch=('x86_64') url='http://blast.ncbi.nlm.nih.gov' license=('custom') diff --git a/BioArchLinux/bowtie/PKGBUILD b/BioArchLinux/bowtie/PKGBUILD index 08ba4f392d..cbbe7ce40f 100644 --- a/BioArchLinux/bowtie/PKGBUILD +++ b/BioArchLinux/bowtie/PKGBUILD @@ -3,7 +3,7 @@ pkgname=bowtie pkgver=1.3.1 pkgrel=3 -pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates" +pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates. doi:10.1186/gb-2009-10-3-r25" url="http://bowtie-bio.sf.net" arch=('x86_64' 'aarch64') license=('PerlArtistic') diff --git a/BioArchLinux/bowtie2/PKGBUILD b/BioArchLinux/bowtie2/PKGBUILD index 86d29fe214..a0533a5a75 100644 --- a/BioArchLinux/bowtie2/PKGBUILD +++ b/BioArchLinux/bowtie2/PKGBUILD @@ -3,7 +3,7 @@ pkgname=bowtie2 pkgver=2.4.4 pkgrel=3 -pkgdesc="Tool for aligning sequencing reads to long reference sequences" +pkgdesc="Tool for aligning sequencing reads to long reference sequences. doi:10.1038/nmeth.1923" arch=('x86_64' 'aarch64') url="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" license=('GPL') diff --git a/BioArchLinux/bwa/PKGBUILD b/BioArchLinux/bwa/PKGBUILD index ad1b9772c4..fd64cc1932 100644 --- a/BioArchLinux/bwa/PKGBUILD +++ b/BioArchLinux/bwa/PKGBUILD @@ -3,7 +3,7 @@ pkgname=bwa pkgver=v0.7.17.r27.g3ddd7b8 pkgrel=2 -pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome" +pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome. doi:10.1093/bioinformatics/btp324" arch=('x86_64') url="http://bio-bwa.sourceforge.net/" license=('GPL3') diff --git a/BioArchLinux/clustal-omega/PKGBUILD b/BioArchLinux/clustal-omega/PKGBUILD index cb07417d27..2b10e02766 100755 --- a/BioArchLinux/clustal-omega/PKGBUILD +++ b/BioArchLinux/clustal-omega/PKGBUILD @@ -3,7 +3,7 @@ pkgname=clustal-omega pkgver=1.2.4 pkgrel=5 -pkgdesc='A general purpose multiple sequence alignment program for protein and DNA/RNA' +pkgdesc='A general purpose multiple sequence alignment program for protein and DNA/RNA. doi:10.1038/msb.2011.75' arch=('x86_64') url='http://www.clustal.org/omega' license=('GPL2') diff --git a/BioArchLinux/clustalw/PKGBUILD b/BioArchLinux/clustalw/PKGBUILD index 79f6433075..18779c911d 100755 --- a/BioArchLinux/clustalw/PKGBUILD +++ b/BioArchLinux/clustalw/PKGBUILD @@ -3,7 +3,7 @@ pkgname=clustalw pkgver=2.1 pkgrel=5 -pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool)' +pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). doi:10.1093/bioinformatics/btm404' arch=('x86_64') url='http://www.clustal.org/clustal2' license=('LGPL3') diff --git a/BioArchLinux/clustalx/PKGBUILD b/BioArchLinux/clustalx/PKGBUILD index 8d6dde3ab0..17f7183611 100755 --- a/BioArchLinux/clustalx/PKGBUILD +++ b/BioArchLinux/clustalx/PKGBUILD @@ -5,7 +5,7 @@ pkgname=clustalx pkgver=2.1 pkgrel=5 -pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool' +pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). doi:10.1093/bioinformatics/btm404' arch=('x86_64') url='http://www.clustal.org/clustal2' license=('LGPL3') diff --git a/BioArchLinux/easycodeml/PKGBUILD b/BioArchLinux/easycodeml/PKGBUILD index bcfb1a69de..25706c539f 100644 --- a/BioArchLinux/easycodeml/PKGBUILD +++ b/BioArchLinux/easycodeml/PKGBUILD @@ -4,7 +4,7 @@ pkgname=easycodeml pkgver=1.21 pkgrel=1 -pkgdesc="A visual tool for analysis of selection using CodeML" +pkgdesc="A visual tool for analysis of selection using CodeML. doi:10.1002/ece3.5015" arch=('x86_64') url="https://github.com/BioEasy/EasyCodeML" license=('LGPL3') diff --git a/BioArchLinux/emboss/PKGBUILD b/BioArchLinux/emboss/PKGBUILD index cf3820ecda..9fe56b7d2d 100644 --- a/BioArchLinux/emboss/PKGBUILD +++ b/BioArchLinux/emboss/PKGBUILD @@ -5,7 +5,7 @@ pkgname=emboss _pkgname=EMBOSS pkgver=6.6.0 pkgrel=6 -pkgdesc="A collection of molecular biology applications" +pkgdesc="A collection of molecular biology applications. doi:10.1016/s0168-9525(00)02024-2" arch=('x86_64' 'i686') url="http://emboss.sourceforge.net/" depends=('gd' 'pcre' 'java-runtime') diff --git a/BioArchLinux/fasttree/PKGBUILD b/BioArchLinux/fasttree/PKGBUILD index f9943e83cd..f69ee78e22 100644 --- a/BioArchLinux/fasttree/PKGBUILD +++ b/BioArchLinux/fasttree/PKGBUILD @@ -2,7 +2,7 @@ pkgname=fasttree pkgver=2.1.9 pkgrel=3 -pkgdesc="Approximately-Maximum-Likelihood Trees for Large Alignments" +pkgdesc="Approximately-Maximum-Likelihood Trees for Large Alignments. doi:10.1371/journal.pone.0009490" arch=(i686 x86_64) url="http://www.microbesonline.org/fasttree/" license=('GPL') diff --git a/BioArchLinux/fastx-toolkit/PKGBUILD b/BioArchLinux/fastx-toolkit/PKGBUILD index 64ce173813..ef69f690f1 100644 --- a/BioArchLinux/fastx-toolkit/PKGBUILD +++ b/BioArchLinux/fastx-toolkit/PKGBUILD @@ -3,7 +3,7 @@ pkgname=fastx-toolkit pkgver=0.0.14 pkgrel=3 -pkgdesc="The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing." +pkgdesc="The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing" arch=("any") url="https://github.com/agordon/fastx_toolkit" license=('AGPL3') diff --git a/BioArchLinux/gblocks/PKGBUILD b/BioArchLinux/gblocks/PKGBUILD index a3c625435e..08a294aeed 100644 --- a/BioArchLinux/gblocks/PKGBUILD +++ b/BioArchLinux/gblocks/PKGBUILD @@ -8,7 +8,7 @@ provides=("gblocks") pkgver=0.91b pkgrel=4 pkgdesc="A program written in ANSI C language that eliminates poorly aligned\ - positions and divergent regions of an alignment of DNA or protein sequences" + positions and divergent regions of an alignment of DNA or protein sequences. doi:10.1093/oxfordjournals.molbev.a026334" url='http://molevol.cmima.csic.es/castresana/Gblocks.html' arch=('x86_64') diff --git a/BioArchLinux/hmmer/PKGBUILD b/BioArchLinux/hmmer/PKGBUILD index 8e2005aec1..72098a83b1 100644 --- a/BioArchLinux/hmmer/PKGBUILD +++ b/BioArchLinux/hmmer/PKGBUILD @@ -5,7 +5,7 @@ pkgname=hmmer pkgver=3.3.2 pkgrel=1 -pkgdesc="Profile hidden Markov models (HMMs) for database searching using consensus sequences" +pkgdesc="Profile hidden Markov models (HMMs) for database searching using consensus sequences. dio:10.1093/bioinformatics/14.9.755" arch=('i686' 'x86_64') checkdepends=('perl-perl4-corelibs' 'python') license=('GPL') diff --git a/BioArchLinux/htslib/PKGBUILD b/BioArchLinux/htslib/PKGBUILD index 0505adf001..7956664b1e 100644 --- a/BioArchLinux/htslib/PKGBUILD +++ b/BioArchLinux/htslib/PKGBUILD @@ -4,7 +4,7 @@ pkgname=htslib pkgver=1.14 pkgrel=4 -pkgdesc='A C library for high-throughput sequencing data formats' +pkgdesc='A C library for high-throughput sequencing data formats. doi:10.1093/gigascience/giab007' arch=('x86_64') url="https://github.com/samtools/${pkgname}" license=('MIT GPL') diff --git a/BioArchLinux/insight-toolkit/PKGBUILD b/BioArchLinux/insight-toolkit/PKGBUILD index fdc9b006a6..15c81c3a91 100644 --- a/BioArchLinux/insight-toolkit/PKGBUILD +++ b/BioArchLinux/insight-toolkit/PKGBUILD @@ -7,7 +7,7 @@ pkgname=insight-toolkit pkgver=5.2.1 pkgrel=17 -pkgdesc='Cross-platform system that provides developers with an extensive suite of software tools for image analysis' +pkgdesc='Cross-platform system that provides developers with an extensive suite of software tools for image analysis. doi:10.3389/fninf.2014.00044' arch=('i686' 'x86_64') url='http://www.itk.org/' license=('APACHE') diff --git a/BioArchLinux/iqtree/PKGBUILD b/BioArchLinux/iqtree/PKGBUILD index 5987267b4b..3ccc98e768 100644 --- a/BioArchLinux/iqtree/PKGBUILD +++ b/BioArchLinux/iqtree/PKGBUILD @@ -9,7 +9,7 @@ pkgname=iqtree pkgver=2.1.3 pkgrel=3 -pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP)" +pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP). doi:10.1093/molbev/msaa015" arch=(x86_64) url="http://www.iqtree.org/" license=('GPL2') diff --git a/BioArchLinux/jane/PKGBUILD b/BioArchLinux/jane/PKGBUILD index a44ac37e5e..5a0cfb263a 100644 --- a/BioArchLinux/jane/PKGBUILD +++ b/BioArchLinux/jane/PKGBUILD @@ -4,7 +4,7 @@ pkgname=jane pkgver=4.01 pkgrel=2 -pkgdesc="software tool for the cophylogeny reconstruction problem" +pkgdesc="software tool for the cophylogeny reconstruction problem. doi:10.1186/1748-7188-5-16" arch=('x86_64') url="https://www.cs.hmc.edu/~hadas/jane/" license=('Harvey Mudd College source code & Apache License') diff --git a/BioArchLinux/jmodeltest/PKGBUILD b/BioArchLinux/jmodeltest/PKGBUILD index 392a047247..01398938ad 100755 --- a/BioArchLinux/jmodeltest/PKGBUILD +++ b/BioArchLinux/jmodeltest/PKGBUILD @@ -5,7 +5,7 @@ pkgname=jmodeltest pkgver=2.1.10r20160303 _pkgver=2.1.10 pkgrel=4 -pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing" +pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing. doi:10.1093/molbev/msn083" arch=('x86_64') provides=("jmodeltest") url="https://github.com/ddarriba/jmodeltest2" diff --git a/BioArchLinux/mafft/PKGBUILD b/BioArchLinux/mafft/PKGBUILD index d37a190fc5..176d37fe9c 100644 --- a/BioArchLinux/mafft/PKGBUILD +++ b/BioArchLinux/mafft/PKGBUILD @@ -5,7 +5,7 @@ pkgname=mafft pkgver=7.487 pkgrel=1 -pkgdesc='Multiple alignment program for amino acid or nucleotide sequences' +pkgdesc='Multiple alignment program for amino acid or nucleotide sequences. doi:10.1093/molbev/mst010' arch=('x86_64') url='https://mafft.cbrc.jp/alignment/software' license=('BSD') diff --git a/BioArchLinux/mega/PKGBUILD b/BioArchLinux/mega/PKGBUILD index 978acd12da..a0df36ee2d 100644 --- a/BioArchLinux/mega/PKGBUILD +++ b/BioArchLinux/mega/PKGBUILD @@ -5,7 +5,7 @@ pkgname=mega _pkgname=mega pkgver=11.0.10 pkgrel=2 -pkgdesc=" Molecular Evolutionary Genetics Analysis" +pkgdesc="Molecular Evolutionary Genetics Analysis. doi:10.1093/molbev/msy096" arch=('x86_64') url="https://megasoftware.net" license=('custom') diff --git a/BioArchLinux/modeltest-ng/PKGBUILD b/BioArchLinux/modeltest-ng/PKGBUILD index e70b856f8a..839a0e7f9d 100644 --- a/BioArchLinux/modeltest-ng/PKGBUILD +++ b/BioArchLinux/modeltest-ng/PKGBUILD @@ -4,7 +4,7 @@ pkgname=modeltest-ng pkgver=0.1.7 pkgrel=4 -pkgdesc="A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models" +pkgdesc="A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. doi:10.1093/molbev/msz189" url='https://github.com/ddarriba/modeltest' arch=('x86_64') license=('GPL3') diff --git a/BioArchLinux/morphoj/PKGBUILD b/BioArchLinux/morphoj/PKGBUILD index bb7cf82138..01747ec906 100644 --- a/BioArchLinux/morphoj/PKGBUILD +++ b/BioArchLinux/morphoj/PKGBUILD @@ -4,7 +4,7 @@ pkgname=morphoj pkgver=1.07a pkgrel=3 -pkgdesc="MorphoJ is an integrated program package for doing geometric morphometrics" +pkgdesc="MorphoJ is an integrated program package for doing geometric morphometrics. doi:10.1111/j.1755-0998.2010.02924.x" arch=('x86_64') depends=( 'java-runtime' diff --git a/BioArchLinux/mrbayes-mpi/PKGBUILD b/BioArchLinux/mrbayes-mpi/PKGBUILD index 526228a41f..de75f222a0 100644 --- a/BioArchLinux/mrbayes-mpi/PKGBUILD +++ b/BioArchLinux/mrbayes-mpi/PKGBUILD @@ -5,7 +5,7 @@ pkgname=mrbayes-mpi pkgver=3.2.7 pkgrel=5 -pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models" +pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. doi:10.1093/sysbio/sys029" arch=('i686' 'x86_64') url="nbisweden.github.io/mrbayes/" license=('GPL3') diff --git a/BioArchLinux/mrbayes/PKGBUILD b/BioArchLinux/mrbayes/PKGBUILD index 9dc7f4325b..6082ec0a3d 100644 --- a/BioArchLinux/mrbayes/PKGBUILD +++ b/BioArchLinux/mrbayes/PKGBUILD @@ -5,7 +5,7 @@ _up_pkgname=MrBayes pkgver=3.2.7 pkgrel=4 provides=("mrbayes") -pkgdesc="A program for the Bayesian estimation of phylogeny" +pkgdesc="A program for the Bayesian estimation of phylogeny. doi:10.1093/sysbio/sys029" arch=('i686' 'x86_64') license=('GPL') url="http://nbisweden.github.io/MrBayes/" diff --git a/BioArchLinux/muscle/PKGBUILD b/BioArchLinux/muscle/PKGBUILD index d57e84e74b..f3aa5b8113 100644 --- a/BioArchLinux/muscle/PKGBUILD +++ b/BioArchLinux/muscle/PKGBUILD @@ -4,7 +4,7 @@ pkgname=muscle pkgver=5.0.1428 pkgrel=5 -pkgdesc="multiple sequence comparison by log-expectation" +pkgdesc="Multiple sequence alignment software enabling improved estimates of phylogenetic tree confidence by ensemble bootstrapping. doi:10.1101/2021.06.20.449169" arch=('i686' 'x86_64') url="http://www.drive5.com/muscle/" license=('GPL3') diff --git a/BioArchLinux/paml/PKGBUILD b/BioArchLinux/paml/PKGBUILD index 7bd14c8e23..b7861f697a 100644 --- a/BioArchLinux/paml/PKGBUILD +++ b/BioArchLinux/paml/PKGBUILD @@ -2,7 +2,7 @@ pkgname=paml pkgver=4.10.1 pkgrel=2 -pkgdesc="Phylogenetic analysis by maximum likelihood" +pkgdesc="Phylogenetic analysis by maximum likelihood. doi:10.1093/molbev/msm088" arch=('x86_64') url="http://abacus.gene.ucl.ac.uk/software/" license=('GPL3') diff --git a/BioArchLinux/paup/PKGBUILD b/BioArchLinux/paup/PKGBUILD index a22c8f3f77..31f4a0ac65 100644 --- a/BioArchLinux/paup/PKGBUILD +++ b/BioArchLinux/paup/PKGBUILD @@ -4,7 +4,7 @@ pkgname=paup pkgver=4a168 _execname=paup${pkgver//.0/}_ubuntu64 pkgrel=4 -pkgdesc="Phylogenetic Analysis Using PAUP" +pkgdesc="Phylogenetic Analysis Using PAUP. doi:10.1002/0471250953.bi0604s00" arch=('i686' 'x86_64') url="http://phylosolutions.com/paup-test/" license=('custom') diff --git a/BioArchLinux/phylip/PKGBUILD b/BioArchLinux/phylip/PKGBUILD index a4f1ffab72..12d555131d 100644 --- a/BioArchLinux/phylip/PKGBUILD +++ b/BioArchLinux/phylip/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phylip pkgver=3.698 pkgrel=4 -pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies" +pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies. doi:10.1111/j.1096-0031.1989.tb00562.x" arch=('i686' 'x86_64') url="http://evolution.genetics.washington.edu/phylip.html" source=(http://evolution.gs.washington.edu/phylip/download/phylip-$pkgver.zip diff --git a/BioArchLinux/phylobayes-mpi/PKGBUILD b/BioArchLinux/phylobayes-mpi/PKGBUILD index a9fdb66298..47b4372c87 100644 --- a/BioArchLinux/phylobayes-mpi/PKGBUILD +++ b/BioArchLinux/phylobayes-mpi/PKGBUILD @@ -4,7 +4,7 @@ _pkgname=phylobayes pkgname=$_pkgname-mpi pkgver=1.8c pkgrel=4 -pkgdesc="phylogenetic reconstruction using infinite mixtures" +pkgdesc="phylogenetic reconstruction using infinite mixtures. doi:10.1093/molbev/msh112" arch=('i686' 'x86_64') url="https://github.com/bayesiancook/pbmpi" license=('GPL2') diff --git a/BioArchLinux/phylobayes/PKGBUILD b/BioArchLinux/phylobayes/PKGBUILD index 430125416b..6ab0748e35 100644 --- a/BioArchLinux/phylobayes/PKGBUILD +++ b/BioArchLinux/phylobayes/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phylobayes pkgver=4.1c pkgrel=3 -pkgdesc="phylogenetic reconstruction using infinite mixtures" +pkgdesc="phylogenetic reconstruction using infinite mixtures. doi:10.1093/molbev/msh112" arch=('i686' 'x86_64') url="https://github.com/bayesiancook/phylobayes" license=('unknow') diff --git a/BioArchLinux/phylonet-hmm/PKGBUILD b/BioArchLinux/phylonet-hmm/PKGBUILD index c3269b0ed8..5352795f56 100644 --- a/BioArchLinux/phylonet-hmm/PKGBUILD +++ b/BioArchLinux/phylonet-hmm/PKGBUILD @@ -9,7 +9,7 @@ depends=( 'java-runtime' ) makedepends=('ant') -pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes" +pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes. doi:10.1371/journal.pcbi.1003649" arch=('x86_64') url="https://bioinfocs.rice.edu/node/108" license=('GPL') diff --git a/BioArchLinux/phylonet/PKGBUILD b/BioArchLinux/phylonet/PKGBUILD index 0218bb0684..4e0be16efc 100644 --- a/BioArchLinux/phylonet/PKGBUILD +++ b/BioArchLinux/phylonet/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="TA suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events" +pkgdesc="TA suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events. doi:10.1093/sysbio/syy015" arch=('x86_64') url="https://bioinfocs.rice.edu/PhyloNet" license=('GPL2') diff --git a/BioArchLinux/phylonium/PKGBUILD b/BioArchLinux/phylonium/PKGBUILD index 4c1342cc16..86aa79b6da 100644 --- a/BioArchLinux/phylonium/PKGBUILD +++ b/BioArchLinux/phylonium/PKGBUILD @@ -2,7 +2,7 @@ pkgname=phylonium pkgver=1.6 pkgrel=1 -pkgdesc="Fast and Accurate Estimation of Evolutionary Distances" +pkgdesc="Fast and Accurate Estimation of Evolutionary Distances. doi:10.1093/bioinformatics/btz903" url="https://github.com/evolbioinf/phylonium/" license=("GPL3") # "custom:ISC" depends=("libdivsufsort") diff --git a/BioArchLinux/phylosuite/PKGBUILD b/BioArchLinux/phylosuite/PKGBUILD index ed5c6de273..0cfda2f415 100644 --- a/BioArchLinux/phylosuite/PKGBUILD +++ b/BioArchLinux/phylosuite/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phylosuite pkgver=1.2.2 pkgrel=4 -pkgdesc="an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies" +pkgdesc="an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. doi:10.1111/1755-0998.13096" arch=('x86_64') url="https://github.com/dongzhang0725/PhyloSuite" license=('GPL3') diff --git a/BioArchLinux/phyml/PKGBUILD b/BioArchLinux/phyml/PKGBUILD index 727a2c7917..2295f48b96 100644 --- a/BioArchLinux/phyml/PKGBUILD +++ b/BioArchLinux/phyml/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phyml pkgver=3.3.20211231 pkgrel=1 epoch=1 -pkgdesc="Builds phylogenies from DNA or protein sequences using a maximum likelihood approach" +pkgdesc="Builds phylogenies from DNA or protein sequences using a maximum likelihood approach. doi:10.1093/sysbio/syq010" arch=('i686' 'x86_64') url="https://github.com/stephaneguindon/phyml" license=('GPL2') diff --git a/BioArchLinux/pibuss/PKGBUILD b/BioArchLinux/pibuss/PKGBUILD index 646ce1b3ee..920386c03f 100644 --- a/BioArchLinux/pibuss/PKGBUILD +++ b/BioArchLinux/pibuss/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication" +pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. doi:10.1186/1471-2105-15-133" arch=('x86_64') url="https://rega.kuleuven.be/cev/ecv/software/pibuss" license=('custom') diff --git a/BioArchLinux/popart/PKGBUILD b/BioArchLinux/popart/PKGBUILD index 92fcfce19d..1e3c6e97c6 100644 --- a/BioArchLinux/popart/PKGBUILD +++ b/BioArchLinux/popart/PKGBUILD @@ -3,7 +3,7 @@ pkgname=popart pkgver=20190715.150937 pkgrel=3 -pkgdesc="free population genetics software" +pkgdesc="Full-feature software for haplotype network reconstruction. doi:10.1111/2041-210X.12410" arch=('x86_64') url="http://popart.otago.ac.nz/index.shtml" license=('LGPLv2') diff --git a/BioArchLinux/primer3/PKGBUILD b/BioArchLinux/primer3/PKGBUILD index cd07210f67..d3a9cf1cf5 100644 --- a/BioArchLinux/primer3/PKGBUILD +++ b/BioArchLinux/primer3/PKGBUILD @@ -3,7 +3,7 @@ pkgname=primer3 pkgver=2.5.0 pkgrel=4 -pkgdesc="Tool to design flanking oligo nucleotides for DNA amplification" +pkgdesc="Tool to design flanking oligo nucleotides for DNA amplification. doi:10.1093/nar/gks596" arch=('i686' 'x86_64') license=('GPL2') depends=('gcc-libs') diff --git a/BioArchLinux/rasp/PKGBUILD b/BioArchLinux/rasp/PKGBUILD index c5366ef8cf..b98450d74e 100644 --- a/BioArchLinux/rasp/PKGBUILD +++ b/BioArchLinux/rasp/PKGBUILD @@ -4,7 +4,7 @@ pkgname=rasp pkgver=20211014 pkgrel=4 -pkgdesc="Reconstruct Ancestral State in Phylogenies is a tool for inferring ancestral state" +pkgdesc="Ancestral state reconstruction tool for multiple genes and characters. doi:10.1093/molbev/msz257" arch=('x86_64') url="http://mnh.scu.edu.cn/soft/blog/rasp/" license=('GPL3') diff --git a/BioArchLinux/raxml-mpi/PKGBUILD b/BioArchLinux/raxml-mpi/PKGBUILD index e24980d96f..70e6dda0d3 100644 --- a/BioArchLinux/raxml-mpi/PKGBUILD +++ b/BioArchLinux/raxml-mpi/PKGBUILD @@ -4,7 +4,7 @@ pkgname=raxml-mpi pkgver=8.2.12 pkgrel=4 -pkgdesc="Randomized Axelerated Maximum Likelihood" +pkgdesc="Randomized Axelerated Maximum Likelihood. doi:10.1093/bioinformatics/btu033" arch=('x86_64') url="http://sco.h-its.org/exelixis/web/software/raxml/" license=('GPL3') diff --git a/BioArchLinux/raxml-ng-mpi/PKGBUILD b/BioArchLinux/raxml-ng-mpi/PKGBUILD index ace196a627..8870f82f33 100644 --- a/BioArchLinux/raxml-ng-mpi/PKGBUILD +++ b/BioArchLinux/raxml-ng-mpi/PKGBUILD @@ -6,7 +6,7 @@ pkgname=raxml-ng-mpi pkgver=1.1.0 _commit=411611611793e53c992717d869ca64370f2e4789 pkgrel=17 -pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion" +pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. doi:10.1093/bioinformatics/btz305" url='https://github.com/amkozlov/raxml-ng' arch=('x86_64') license=('AGPL3') diff --git a/BioArchLinux/raxml-ng/PKGBUILD b/BioArchLinux/raxml-ng/PKGBUILD index 1b934f8d03..9fec3bfad8 100644 --- a/BioArchLinux/raxml-ng/PKGBUILD +++ b/BioArchLinux/raxml-ng/PKGBUILD @@ -5,7 +5,7 @@ pkgname=raxml-ng pkgver=1.1.0 _commit=411611611793e53c992717d869ca64370f2e4789 pkgrel=16 -pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion" +pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. doi:10.1093/bioinformatics/btz305" url='https://github.com/amkozlov/raxml-ng' arch=('x86_64') license=('AGPL3') diff --git a/BioArchLinux/raxml/PKGBUILD b/BioArchLinux/raxml/PKGBUILD index 01d6937050..32f76ad7a3 100644 --- a/BioArchLinux/raxml/PKGBUILD +++ b/BioArchLinux/raxml/PKGBUILD @@ -3,7 +3,7 @@ pkgname=raxml pkgver=8.2.12 pkgrel=4 -pkgdesc="Randomized Axelerated Maximum Likelihood" +pkgdesc="Randomized Axelerated Maximum Likelihood. doi:10.1093/bioinformatics/btu033" arch=('x86_64') url="http://sco.h-its.org/exelixis/web/software/raxml/" license=('GPL3') diff --git a/BioArchLinux/raxmlgui/PKGBUILD b/BioArchLinux/raxmlgui/PKGBUILD index 8aef181906..8f60eeec0d 100644 --- a/BioArchLinux/raxmlgui/PKGBUILD +++ b/BioArchLinux/raxmlgui/PKGBUILD @@ -4,7 +4,7 @@ pkgname=raxmlgui pkgver=2.0.6 pkgrel=2 -pkgdesc="A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis" +pkgdesc="A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis. doi:10.1111/2041-210X.13512" arch=('x86_64') url="https://antonellilab.github.io/raxmlGUI" provides=("raxmlgui") diff --git a/BioArchLinux/samtools/PKGBUILD b/BioArchLinux/samtools/PKGBUILD index 703a2cef6f..4c4ff427fd 100644 --- a/BioArchLinux/samtools/PKGBUILD +++ b/BioArchLinux/samtools/PKGBUILD @@ -7,7 +7,7 @@ pkgname=samtools pkgver=1.14 pkgrel=4 -pkgdesc="tools for manipulating next-generation sequencing data" +pkgdesc="tools for manipulating next-generation sequencing data. doi:10.1093/bioinformatics/btp352" arch=('i686' 'x86_64') url="http://www.htslib.org/" license=('custom') diff --git a/BioArchLinux/seaview/PKGBUILD b/BioArchLinux/seaview/PKGBUILD index 72a3f0a122..67538e2506 100644 --- a/BioArchLinux/seaview/PKGBUILD +++ b/BioArchLinux/seaview/PKGBUILD @@ -4,7 +4,7 @@ pkgname=seaview pkgver=5.0.5 pkgrel=3 -pkgdesc="GUI for multiple sequence alignment and molecular phylogeny" +pkgdesc="GUI for multiple sequence alignment and molecular phylogeny. doi:10.1093/molbev/msp259" arch=('x86_64') url="http://doua.prabi.fr/software/seaview" license=('GPL3') diff --git a/BioArchLinux/seqan/PKGBUILD b/BioArchLinux/seqan/PKGBUILD index b3c75f5612..489191bc92 100644 --- a/BioArchLinux/seqan/PKGBUILD +++ b/BioArchLinux/seqan/PKGBUILD @@ -1,7 +1,7 @@ pkgname=seqan pkgver=2.4.0 pkgrel=4 -pkgdesc="SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data" +pkgdesc="SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. doi:10.1186/1471-2105-9-11" arch=("any") url="http://www.seqan.de" license=('custom') diff --git a/BioArchLinux/seqan3/PKGBUILD b/BioArchLinux/seqan3/PKGBUILD index a792b0f25f..eac77d1518 100644 --- a/BioArchLinux/seqan3/PKGBUILD +++ b/BioArchLinux/seqan3/PKGBUILD @@ -1,7 +1,7 @@ pkgname=seqan3 pkgver=3.1.0 pkgrel=4 -pkgdesc="The modern C++ library for sequence analysis. Contains version 3 of the library and API docs." +pkgdesc="The modern C++ library for sequence analysis. Contains version 3 of the library and API docs. doi:10.1016/j.jbiotec.2017.07.017" arch=("any") url="http://www.seqan.de" license=('custom') diff --git a/BioArchLinux/spread/PKGBUILD b/BioArchLinux/spread/PKGBUILD index 24761456f6..91b0e8ee39 100644 --- a/BioArchLinux/spread/PKGBUILD +++ b/BioArchLinux/spread/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion" +pkgdesc="a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion. doi:10.1093/bioinformatics/btr481" arch=('x86_64') url="https://rega.kuleuven.be/cev/ecv/software/${pkgname}" license=('custom') diff --git a/BioArchLinux/spread3/PKGBUILD b/BioArchLinux/spread3/PKGBUILD index a1d7fa4dc7..d4d14737d8 100644 --- a/BioArchLinux/spread3/PKGBUILD +++ b/BioArchLinux/spread3/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes" +pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes. doi:10.1093/molbev/msw082" arch=('x86_64') url="https://rega.kuleuven.be/cev/ecv/software/SpreaD3" license=('custom') diff --git a/BioArchLinux/tempest/PKGBUILD b/BioArchLinux/tempest/PKGBUILD index fdfe31aa53..83e68b4636 100644 --- a/BioArchLinux/tempest/PKGBUILD +++ b/BioArchLinux/tempest/PKGBUILD @@ -7,7 +7,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies" +pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. doi:10.1093/ve/vew007" arch=('x86_64') url="http://tree.bio.ed.ac.uk/software/tempest/" license=('GPL2') diff --git a/BioArchLinux/tiger/PKGBUILD b/BioArchLinux/tiger/PKGBUILD index cb998d7a87..9b5521ce10 100644 --- a/BioArchLinux/tiger/PKGBUILD +++ b/BioArchLinux/tiger/PKGBUILD @@ -4,7 +4,7 @@ pkgname=tiger pkgver=1.02 pkgrel=4 -pkgdesc="Identifying rapidly-evolving characters in evolutionary data" +pkgdesc="Identifying rapidly-evolving characters in evolutionary data. doi:10.1093/sysbio/syr064" arch=('x86_64') url="http://mcinerneylab.com/software/tiger/","" license=('GPL3') diff --git a/BioArchLinux/tnt-gui/PKGBUILD b/BioArchLinux/tnt-gui/PKGBUILD index b269e2384f..10d88a045d 100644 --- a/BioArchLinux/tnt-gui/PKGBUILD +++ b/BioArchLinux/tnt-gui/PKGBUILD @@ -4,7 +4,7 @@ pkgname=tnt-gui pkgver=2021.12.27 pkgrel=1 -pkgdesc="Tree analysis using New Technology" +pkgdesc="Tree analysis using New Technology. doi:10.1111/cla.12160" arch=('x86_64') url="http://www.lillo.org.ar/phylogeny/tnt/" license=('custom') diff --git a/BioArchLinux/tnt-mpi/PKGBUILD b/BioArchLinux/tnt-mpi/PKGBUILD index ffbb995696..6f8f87572a 100644 --- a/BioArchLinux/tnt-mpi/PKGBUILD +++ b/BioArchLinux/tnt-mpi/PKGBUILD @@ -5,7 +5,7 @@ pkgname=tnt-mpi _pkgname=mpitnt pkgver=2021.12.27 pkgrel=1 -pkgdesc="Tree analysis using New Technology" +pkgdesc="Tree analysis using New Technology. doi:10.1111/cla.12160" arch=('x86_64') url="http://www.lillo.org.ar/phylogeny/tnt/" provides=('tnt') diff --git a/BioArchLinux/tnt/PKGBUILD b/BioArchLinux/tnt/PKGBUILD index e027f8b59a..e573ecbe2c 100644 --- a/BioArchLinux/tnt/PKGBUILD +++ b/BioArchLinux/tnt/PKGBUILD @@ -4,7 +4,7 @@ pkgname=tnt pkgver=2021.12.27 pkgrel=1 -pkgdesc="Tree analysis using New Technology" +pkgdesc="Tree analysis using New Technology. doi:10.1111/cla.12160" arch=('x86_64') url="http://www.lillo.org.ar/phylogeny/tnt/" provides=('tnt') diff --git a/BioArchLinux/tracer/PKGBUILD b/BioArchLinux/tracer/PKGBUILD index 594f2a3224..e6025f7114 100644 --- a/BioArchLinux/tracer/PKGBUILD +++ b/BioArchLinux/tracer/PKGBUILD @@ -5,7 +5,7 @@ pkgname=tracer _pkgname=Tracer pkgver=1.7.2 pkgrel=3 -pkgdesc="Posterior summarisation in Bayesian phylogenetics" +pkgdesc="Posterior summarisation in Bayesian phylogenetics. doi:10.1093/sysbio/syy032" arch=('x86_64') url="https://github.com/beast-dev/tracer" license=('unknown') diff --git a/BioArchLinux/tracy/PKGBUILD b/BioArchLinux/tracy/PKGBUILD index d71b99f390..3ebc616441 100644 --- a/BioArchLinux/tracy/PKGBUILD +++ b/BioArchLinux/tracy/PKGBUILD @@ -3,7 +3,7 @@ pkgname=tracy pkgver=0.6.1 pkgrel=4 -pkgdesc="Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files" +pkgdesc="Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files. doi:10.1186/s12864-020-6635-8" arch=('x86_64') url="https://github.com/gear-genomics/tracy" license=('BSDv3') diff --git a/BioArchLinux/trimal/PKGBUILD b/BioArchLinux/trimal/PKGBUILD index 85bc94c4ef..dd542f4e00 100644 --- a/BioArchLinux/trimal/PKGBUILD +++ b/BioArchLinux/trimal/PKGBUILD @@ -2,7 +2,7 @@ pkgname=trimal pkgver=1.4.1 pkgrel=6 -pkgdesc="A tool for automated alignment trimming in large-scale phylogenetic analyses" +pkgdesc="A tool for automated alignment trimming in large-scale phylogenetic analyses. doi:10.1093/bioinformatics/btp348" arch=('x86_64') url="trimal.cgenomics.org" license=('GPL') diff --git a/BioArchLinux/ugene/PKGBUILD b/BioArchLinux/ugene/PKGBUILD index 51f692f909..3ddf8fa38c 100644 --- a/BioArchLinux/ugene/PKGBUILD +++ b/BioArchLinux/ugene/PKGBUILD @@ -4,7 +4,7 @@ pkgname=ugene pkgver=41.0 pkgrel=3 -pkgdesc="A free cross-platform genome analysis suite" +pkgdesc="A free cross-platform genome analysis suite. doi:10.1093/bioinformatics/bts091" arch=('x86_64') url="http://ugene.net" license=('GPL') diff --git a/BioArchLinux/vcftools/PKGBUILD b/BioArchLinux/vcftools/PKGBUILD index 4a84c3e3f0..246a54e4f0 100644 --- a/BioArchLinux/vcftools/PKGBUILD +++ b/BioArchLinux/vcftools/PKGBUILD @@ -4,7 +4,7 @@ pkgname=vcftools pkgver=0.1.16 pkgrel=4 -pkgdesc="A set of tools written in Perl and C++ for working with VCF files" +pkgdesc="A set of tools written in Perl and C++ for working with VCF files. doi:10.1093/bioinformatics/btr330" arch=('x86_64') url="https://vcftools.github.io/" license=('LGPL3') From 18b863f72d01558a3c0a1bd20c5e2fd57b61ed0c Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Mon, 3 Jan 2022 23:13:03 +0100 Subject: [PATCH 05/10] Changed DOI to direct doi.org links --- BioArchLinux/avogadro2/PKGBUILD | 2 +- BioArchLinux/bali-phy/PKGBUILD | 2 +- BioArchLinux/beast/PKGBUILD | 2 +- BioArchLinux/beast2/PKGBUILD | 2 +- BioArchLinux/blast+/PKGBUILD | 2 +- BioArchLinux/bowtie/PKGBUILD | 2 +- BioArchLinux/bowtie2/PKGBUILD | 2 +- BioArchLinux/bwa/PKGBUILD | 2 +- BioArchLinux/clustal-omega/PKGBUILD | 2 +- BioArchLinux/clustalw/PKGBUILD | 2 +- BioArchLinux/clustalx/PKGBUILD | 2 +- BioArchLinux/easycodeml/PKGBUILD | 2 +- BioArchLinux/emboss/PKGBUILD | 2 +- BioArchLinux/fasttree/PKGBUILD | 2 +- BioArchLinux/gblocks/PKGBUILD | 2 +- BioArchLinux/gsalign/PKGBUILD | 2 +- BioArchLinux/htslib/PKGBUILD | 2 +- BioArchLinux/insight-toolkit/PKGBUILD | 2 +- BioArchLinux/iqtree/PKGBUILD | 2 +- BioArchLinux/jane/PKGBUILD | 2 +- BioArchLinux/jmodeltest/PKGBUILD | 2 +- BioArchLinux/lra/PKGBUILD | 2 +- BioArchLinux/mafft/PKGBUILD | 2 +- BioArchLinux/mega/PKGBUILD | 2 +- BioArchLinux/minimap2/PKGBUILD | 2 +- BioArchLinux/modeltest-ng/PKGBUILD | 2 +- BioArchLinux/morphoj/PKGBUILD | 2 +- BioArchLinux/mrbayes-mpi/PKGBUILD | 2 +- BioArchLinux/mrbayes/PKGBUILD | 2 +- BioArchLinux/muscle/PKGBUILD | 2 +- BioArchLinux/paml/PKGBUILD | 2 +- BioArchLinux/paup/PKGBUILD | 2 +- BioArchLinux/phylip/PKGBUILD | 2 +- BioArchLinux/phylobayes-mpi/PKGBUILD | 2 +- BioArchLinux/phylobayes/PKGBUILD | 2 +- BioArchLinux/phylonet-hmm/PKGBUILD | 2 +- BioArchLinux/phylonet/PKGBUILD | 2 +- BioArchLinux/phylonium/PKGBUILD | 2 +- BioArchLinux/phylosuite/PKGBUILD | 2 +- BioArchLinux/phyml/PKGBUILD | 2 +- BioArchLinux/pibuss/PKGBUILD | 2 +- BioArchLinux/popart/PKGBUILD | 2 +- BioArchLinux/primer3/PKGBUILD | 2 +- BioArchLinux/rasp/PKGBUILD | 2 +- BioArchLinux/raxml-mpi/PKGBUILD | 2 +- BioArchLinux/raxml-ng-mpi/PKGBUILD | 2 +- BioArchLinux/raxml-ng/PKGBUILD | 2 +- BioArchLinux/raxml/PKGBUILD | 2 +- BioArchLinux/raxmlgui/PKGBUILD | 2 +- BioArchLinux/samtools/PKGBUILD | 2 +- BioArchLinux/seaview/PKGBUILD | 2 +- BioArchLinux/seqan/PKGBUILD | 2 +- BioArchLinux/seqan3/PKGBUILD | 2 +- BioArchLinux/spread/PKGBUILD | 2 +- BioArchLinux/spread3/PKGBUILD | 2 +- BioArchLinux/tempest/PKGBUILD | 2 +- BioArchLinux/tiger/PKGBUILD | 2 +- BioArchLinux/tnt-gui/PKGBUILD | 2 +- BioArchLinux/tnt-mpi/PKGBUILD | 2 +- BioArchLinux/tnt/PKGBUILD | 2 +- BioArchLinux/tracer/PKGBUILD | 2 +- BioArchLinux/tracy/PKGBUILD | 2 +- BioArchLinux/trimal/PKGBUILD | 2 +- BioArchLinux/ugene/PKGBUILD | 2 +- BioArchLinux/vcftools/PKGBUILD | 2 +- 65 files changed, 65 insertions(+), 65 deletions(-) diff --git a/BioArchLinux/avogadro2/PKGBUILD b/BioArchLinux/avogadro2/PKGBUILD index 542c8d62bb..5eb712c89c 100644 --- a/BioArchLinux/avogadro2/PKGBUILD +++ b/BioArchLinux/avogadro2/PKGBUILD @@ -5,7 +5,7 @@ pkgname=avogadro2 _pkgname=avogadroapp pkgver=1.95.1 pkgrel=5 -pkgdesc="An advanced molecular editor. doi:10.1186/1758-2946-4-17" +pkgdesc="An advanced molecular editor. https://doi.org/10.1186/1758-2946-4-17" arch=('x86_64') url="https://two.avogadro.cc" license=('BSD') diff --git a/BioArchLinux/bali-phy/PKGBUILD b/BioArchLinux/bali-phy/PKGBUILD index d98d8fdf55..040c83a9a3 100644 --- a/BioArchLinux/bali-phy/PKGBUILD +++ b/BioArchLinux/bali-phy/PKGBUILD @@ -2,7 +2,7 @@ pkgname=bali-phy pkgver=3.6.1 pkgrel=4 -pkgdesc="Bayesian co-estimation of phylogenies and multiple alignments via MCMC. doi:10.1093/bioinformatics/btab129" +pkgdesc="Bayesian co-estimation of phylogenies and multiple alignments via MCMC. https://doi.org/10.1093/bioinformatics/btab129" arch=('x86_64') url="http://www.bali-phy.org/" license=('GPL') diff --git a/BioArchLinux/beast/PKGBUILD b/BioArchLinux/beast/PKGBUILD index 0c562ede1d..2c1e058786 100644 --- a/BioArchLinux/beast/PKGBUILD +++ b/BioArchLinux/beast/PKGBUILD @@ -5,7 +5,7 @@ pkgname=beast pkgver=1.10.4 pkgrel=8 provides=("beast") -pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. doi:10.1186/1471-2148-7-214" +pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214" arch=('x86_64') url="http://beast.community/" license=('LGPL-2.1 License') diff --git a/BioArchLinux/beast2/PKGBUILD b/BioArchLinux/beast2/PKGBUILD index 0605526843..3e9f4bc4ee 100644 --- a/BioArchLinux/beast2/PKGBUILD +++ b/BioArchLinux/beast2/PKGBUILD @@ -4,7 +4,7 @@ pkgname=beast2 pkgver=2.6.6 pkgrel=3 -pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. 10.1371/journal.pcbi.1003537" +pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. https://doi.org/10.1371/journal.pcbi.1003537" arch=('x86_64') url="http://www.beast2.org/" license=('LGPL-2.1 License') diff --git a/BioArchLinux/blast+/PKGBUILD b/BioArchLinux/blast+/PKGBUILD index ec30032d49..f6de8e086a 100755 --- a/BioArchLinux/blast+/PKGBUILD +++ b/BioArchLinux/blast+/PKGBUILD @@ -5,7 +5,7 @@ pkgname=blast+ pkgver=2.12.0 pkgrel=4 -pkgdesc='BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc). doi:10.1186/1471-2105-10-421' +pkgdesc='BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc). https://doi.org/10.1186/1471-2105-10-421' arch=('x86_64') url='http://blast.ncbi.nlm.nih.gov' license=('custom') diff --git a/BioArchLinux/bowtie/PKGBUILD b/BioArchLinux/bowtie/PKGBUILD index cbbe7ce40f..f78e0b8f9b 100644 --- a/BioArchLinux/bowtie/PKGBUILD +++ b/BioArchLinux/bowtie/PKGBUILD @@ -3,7 +3,7 @@ pkgname=bowtie pkgver=1.3.1 pkgrel=3 -pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates. doi:10.1186/gb-2009-10-3-r25" +pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates. https://doi.org/10.1186/gb-2009-10-3-r25" url="http://bowtie-bio.sf.net" arch=('x86_64' 'aarch64') license=('PerlArtistic') diff --git a/BioArchLinux/bowtie2/PKGBUILD b/BioArchLinux/bowtie2/PKGBUILD index a0533a5a75..0ee0b8a634 100644 --- a/BioArchLinux/bowtie2/PKGBUILD +++ b/BioArchLinux/bowtie2/PKGBUILD @@ -3,7 +3,7 @@ pkgname=bowtie2 pkgver=2.4.4 pkgrel=3 -pkgdesc="Tool for aligning sequencing reads to long reference sequences. doi:10.1038/nmeth.1923" +pkgdesc="Tool for aligning sequencing reads to long reference sequences. https://doi.org/10.1038/nmeth.1923" arch=('x86_64' 'aarch64') url="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" license=('GPL') diff --git a/BioArchLinux/bwa/PKGBUILD b/BioArchLinux/bwa/PKGBUILD index fd64cc1932..d6e5f18577 100644 --- a/BioArchLinux/bwa/PKGBUILD +++ b/BioArchLinux/bwa/PKGBUILD @@ -3,7 +3,7 @@ pkgname=bwa pkgver=v0.7.17.r27.g3ddd7b8 pkgrel=2 -pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome. doi:10.1093/bioinformatics/btp324" +pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome. https://doi.org/10.1093/bioinformatics/btp324" arch=('x86_64') url="http://bio-bwa.sourceforge.net/" license=('GPL3') diff --git a/BioArchLinux/clustal-omega/PKGBUILD b/BioArchLinux/clustal-omega/PKGBUILD index 2b10e02766..2f44a41417 100755 --- a/BioArchLinux/clustal-omega/PKGBUILD +++ b/BioArchLinux/clustal-omega/PKGBUILD @@ -3,7 +3,7 @@ pkgname=clustal-omega pkgver=1.2.4 pkgrel=5 -pkgdesc='A general purpose multiple sequence alignment program for protein and DNA/RNA. doi:10.1038/msb.2011.75' +pkgdesc='A general purpose multiple sequence alignment program for protein and DNA/RNA. https://doi.org/10.1038/msb.2011.75' arch=('x86_64') url='http://www.clustal.org/omega' license=('GPL2') diff --git a/BioArchLinux/clustalw/PKGBUILD b/BioArchLinux/clustalw/PKGBUILD index 18779c911d..baa6d01573 100755 --- a/BioArchLinux/clustalw/PKGBUILD +++ b/BioArchLinux/clustalw/PKGBUILD @@ -3,7 +3,7 @@ pkgname=clustalw pkgver=2.1 pkgrel=5 -pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). doi:10.1093/bioinformatics/btm404' +pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). https://doi.org/10.1093/bioinformatics/btm404' arch=('x86_64') url='http://www.clustal.org/clustal2' license=('LGPL3') diff --git a/BioArchLinux/clustalx/PKGBUILD b/BioArchLinux/clustalx/PKGBUILD index 17f7183611..f49882ee7f 100755 --- a/BioArchLinux/clustalx/PKGBUILD +++ b/BioArchLinux/clustalx/PKGBUILD @@ -5,7 +5,7 @@ pkgname=clustalx pkgver=2.1 pkgrel=5 -pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). doi:10.1093/bioinformatics/btm404' +pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). https://doi.org/10.1093/bioinformatics/btm404' arch=('x86_64') url='http://www.clustal.org/clustal2' license=('LGPL3') diff --git a/BioArchLinux/easycodeml/PKGBUILD b/BioArchLinux/easycodeml/PKGBUILD index 25706c539f..9e1bbc0291 100644 --- a/BioArchLinux/easycodeml/PKGBUILD +++ b/BioArchLinux/easycodeml/PKGBUILD @@ -4,7 +4,7 @@ pkgname=easycodeml pkgver=1.21 pkgrel=1 -pkgdesc="A visual tool for analysis of selection using CodeML. doi:10.1002/ece3.5015" +pkgdesc="A visual tool for analysis of selection using CodeML. https://doi.org/10.1002/ece3.5015" arch=('x86_64') url="https://github.com/BioEasy/EasyCodeML" license=('LGPL3') diff --git a/BioArchLinux/emboss/PKGBUILD b/BioArchLinux/emboss/PKGBUILD index 9fe56b7d2d..c44a74177b 100644 --- a/BioArchLinux/emboss/PKGBUILD +++ b/BioArchLinux/emboss/PKGBUILD @@ -5,7 +5,7 @@ pkgname=emboss _pkgname=EMBOSS pkgver=6.6.0 pkgrel=6 -pkgdesc="A collection of molecular biology applications. doi:10.1016/s0168-9525(00)02024-2" +pkgdesc="A collection of molecular biology applications. https://doi.org/10.1016/s0168-9525(00)02024-2" arch=('x86_64' 'i686') url="http://emboss.sourceforge.net/" depends=('gd' 'pcre' 'java-runtime') diff --git a/BioArchLinux/fasttree/PKGBUILD b/BioArchLinux/fasttree/PKGBUILD index f69ee78e22..a4c019f6bd 100644 --- a/BioArchLinux/fasttree/PKGBUILD +++ b/BioArchLinux/fasttree/PKGBUILD @@ -2,7 +2,7 @@ pkgname=fasttree pkgver=2.1.9 pkgrel=3 -pkgdesc="Approximately-Maximum-Likelihood Trees for Large Alignments. doi:10.1371/journal.pone.0009490" +pkgdesc="Approximately-Maximum-Likelihood Trees for Large Alignments. https://doi.org/10.1371/journal.pone.0009490" arch=(i686 x86_64) url="http://www.microbesonline.org/fasttree/" license=('GPL') diff --git a/BioArchLinux/gblocks/PKGBUILD b/BioArchLinux/gblocks/PKGBUILD index 08a294aeed..48597529bc 100644 --- a/BioArchLinux/gblocks/PKGBUILD +++ b/BioArchLinux/gblocks/PKGBUILD @@ -8,7 +8,7 @@ provides=("gblocks") pkgver=0.91b pkgrel=4 pkgdesc="A program written in ANSI C language that eliminates poorly aligned\ - positions and divergent regions of an alignment of DNA or protein sequences. doi:10.1093/oxfordjournals.molbev.a026334" + positions and divergent regions of an alignment of DNA or protein sequences. https://doi.org/10.1093/oxfordjournals.molbev.a026334" url='http://molevol.cmima.csic.es/castresana/Gblocks.html' arch=('x86_64') diff --git a/BioArchLinux/gsalign/PKGBUILD b/BioArchLinux/gsalign/PKGBUILD index eceeb3a267..274a937705 100644 --- a/BioArchLinux/gsalign/PKGBUILD +++ b/BioArchLinux/gsalign/PKGBUILD @@ -5,7 +5,7 @@ pkgname=gsalign pkgnamecaps=GSAlign pkgver=1.0.22 pkgrel=1 -pkgdesc='An ultra-fast sequence alignment algorithm for intra-species genome comparison. doi:10.1186/s12864-020-6569-1' +pkgdesc='An ultra-fast sequence alignment algorithm for intra-species genome comparison. https://doi.org/10.1186/s12864-020-6569-1' arch=('x86_64') url="https://github.com/hsinnan75/${pkgnamecaps}" license=('MIT') diff --git a/BioArchLinux/htslib/PKGBUILD b/BioArchLinux/htslib/PKGBUILD index 7956664b1e..1c9a27c41a 100644 --- a/BioArchLinux/htslib/PKGBUILD +++ b/BioArchLinux/htslib/PKGBUILD @@ -4,7 +4,7 @@ pkgname=htslib pkgver=1.14 pkgrel=4 -pkgdesc='A C library for high-throughput sequencing data formats. doi:10.1093/gigascience/giab007' +pkgdesc='A C library for high-throughput sequencing data formats. https://doi.org/10.1093/gigascience/giab007' arch=('x86_64') url="https://github.com/samtools/${pkgname}" license=('MIT GPL') diff --git a/BioArchLinux/insight-toolkit/PKGBUILD b/BioArchLinux/insight-toolkit/PKGBUILD index 15c81c3a91..656f1134ca 100644 --- a/BioArchLinux/insight-toolkit/PKGBUILD +++ b/BioArchLinux/insight-toolkit/PKGBUILD @@ -7,7 +7,7 @@ pkgname=insight-toolkit pkgver=5.2.1 pkgrel=17 -pkgdesc='Cross-platform system that provides developers with an extensive suite of software tools for image analysis. doi:10.3389/fninf.2014.00044' +pkgdesc='Cross-platform system that provides developers with an extensive suite of software tools for image analysis. https://doi.org/10.3389/fninf.2014.00044' arch=('i686' 'x86_64') url='http://www.itk.org/' license=('APACHE') diff --git a/BioArchLinux/iqtree/PKGBUILD b/BioArchLinux/iqtree/PKGBUILD index 3ccc98e768..c438a19313 100644 --- a/BioArchLinux/iqtree/PKGBUILD +++ b/BioArchLinux/iqtree/PKGBUILD @@ -9,7 +9,7 @@ pkgname=iqtree pkgver=2.1.3 pkgrel=3 -pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP). doi:10.1093/molbev/msaa015" +pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP). https://doi.org/10.1093/molbev/msaa015" arch=(x86_64) url="http://www.iqtree.org/" license=('GPL2') diff --git a/BioArchLinux/jane/PKGBUILD b/BioArchLinux/jane/PKGBUILD index 5a0cfb263a..683fc82ad3 100644 --- a/BioArchLinux/jane/PKGBUILD +++ b/BioArchLinux/jane/PKGBUILD @@ -4,7 +4,7 @@ pkgname=jane pkgver=4.01 pkgrel=2 -pkgdesc="software tool for the cophylogeny reconstruction problem. doi:10.1186/1748-7188-5-16" +pkgdesc="software tool for the cophylogeny reconstruction problem. https://doi.org/10.1186/1748-7188-5-16" arch=('x86_64') url="https://www.cs.hmc.edu/~hadas/jane/" license=('Harvey Mudd College source code & Apache License') diff --git a/BioArchLinux/jmodeltest/PKGBUILD b/BioArchLinux/jmodeltest/PKGBUILD index 01398938ad..f152dc4a7d 100755 --- a/BioArchLinux/jmodeltest/PKGBUILD +++ b/BioArchLinux/jmodeltest/PKGBUILD @@ -5,7 +5,7 @@ pkgname=jmodeltest pkgver=2.1.10r20160303 _pkgver=2.1.10 pkgrel=4 -pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing. doi:10.1093/molbev/msn083" +pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing. https://doi.org/10.1093/molbev/msn083" arch=('x86_64') provides=("jmodeltest") url="https://github.com/ddarriba/jmodeltest2" diff --git a/BioArchLinux/lra/PKGBUILD b/BioArchLinux/lra/PKGBUILD index fc843bc00e..a83255bdf0 100644 --- a/BioArchLinux/lra/PKGBUILD +++ b/BioArchLinux/lra/PKGBUILD @@ -4,7 +4,7 @@ pkgname=lra pkgver=1.3.2 pkgrel=1 -pkgdesc='A long read aligner for sequences and contigs. doi:10.1371/journal.pcbi.1009078' +pkgdesc='A long read aligner for sequences and contigs. https://doi.org/10.1371/journal.pcbi.1009078' arch=('x86_64') url="https://github.com/ChaissonLab/${pkgname^^}" license=('USC-RL v1.0') diff --git a/BioArchLinux/mafft/PKGBUILD b/BioArchLinux/mafft/PKGBUILD index 176d37fe9c..8bf84f5347 100644 --- a/BioArchLinux/mafft/PKGBUILD +++ b/BioArchLinux/mafft/PKGBUILD @@ -5,7 +5,7 @@ pkgname=mafft pkgver=7.487 pkgrel=1 -pkgdesc='Multiple alignment program for amino acid or nucleotide sequences. doi:10.1093/molbev/mst010' +pkgdesc='Multiple alignment program for amino acid or nucleotide sequences. https://doi.org/10.1093/molbev/mst010' arch=('x86_64') url='https://mafft.cbrc.jp/alignment/software' license=('BSD') diff --git a/BioArchLinux/mega/PKGBUILD b/BioArchLinux/mega/PKGBUILD index a0df36ee2d..fa441e1724 100644 --- a/BioArchLinux/mega/PKGBUILD +++ b/BioArchLinux/mega/PKGBUILD @@ -5,7 +5,7 @@ pkgname=mega _pkgname=mega pkgver=11.0.10 pkgrel=2 -pkgdesc="Molecular Evolutionary Genetics Analysis. doi:10.1093/molbev/msy096" +pkgdesc="Molecular Evolutionary Genetics Analysis. https://doi.org/10.1093/molbev/msy096" arch=('x86_64') url="https://megasoftware.net" license=('custom') diff --git a/BioArchLinux/minimap2/PKGBUILD b/BioArchLinux/minimap2/PKGBUILD index e5d4af08f7..98e77b5e11 100644 --- a/BioArchLinux/minimap2/PKGBUILD +++ b/BioArchLinux/minimap2/PKGBUILD @@ -4,7 +4,7 @@ pkgname=minimap2 pkgver=2.24 pkgrel=1 -pkgdesc='A versatile pairwise aligner for genomic and spliced nucleotide sequences. doi:10.1093/bioinformatics/bty191' +pkgdesc='A versatile pairwise aligner for genomic and spliced nucleotide sequences. https://doi.org/10.1093/bioinformatics/bty191' arch=('x86_64') url="https://github.com/lh3/${pkgname}" license=('MIT') diff --git a/BioArchLinux/modeltest-ng/PKGBUILD b/BioArchLinux/modeltest-ng/PKGBUILD index 839a0e7f9d..09441c4c0c 100644 --- a/BioArchLinux/modeltest-ng/PKGBUILD +++ b/BioArchLinux/modeltest-ng/PKGBUILD @@ -4,7 +4,7 @@ pkgname=modeltest-ng pkgver=0.1.7 pkgrel=4 -pkgdesc="A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. doi:10.1093/molbev/msz189" +pkgdesc="A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. https://doi.org/10.1093/molbev/msz189" url='https://github.com/ddarriba/modeltest' arch=('x86_64') license=('GPL3') diff --git a/BioArchLinux/morphoj/PKGBUILD b/BioArchLinux/morphoj/PKGBUILD index 01747ec906..355fde69dc 100644 --- a/BioArchLinux/morphoj/PKGBUILD +++ b/BioArchLinux/morphoj/PKGBUILD @@ -4,7 +4,7 @@ pkgname=morphoj pkgver=1.07a pkgrel=3 -pkgdesc="MorphoJ is an integrated program package for doing geometric morphometrics. doi:10.1111/j.1755-0998.2010.02924.x" +pkgdesc="MorphoJ is an integrated program package for doing geometric morphometrics. https://doi.org/10.1111/j.1755-0998.2010.02924.x" arch=('x86_64') depends=( 'java-runtime' diff --git a/BioArchLinux/mrbayes-mpi/PKGBUILD b/BioArchLinux/mrbayes-mpi/PKGBUILD index de75f222a0..7abc6ec385 100644 --- a/BioArchLinux/mrbayes-mpi/PKGBUILD +++ b/BioArchLinux/mrbayes-mpi/PKGBUILD @@ -5,7 +5,7 @@ pkgname=mrbayes-mpi pkgver=3.2.7 pkgrel=5 -pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. doi:10.1093/sysbio/sys029" +pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. https://doi.org/10.1093/sysbio/sys029" arch=('i686' 'x86_64') url="nbisweden.github.io/mrbayes/" license=('GPL3') diff --git a/BioArchLinux/mrbayes/PKGBUILD b/BioArchLinux/mrbayes/PKGBUILD index 6082ec0a3d..03ca4a46b2 100644 --- a/BioArchLinux/mrbayes/PKGBUILD +++ b/BioArchLinux/mrbayes/PKGBUILD @@ -5,7 +5,7 @@ _up_pkgname=MrBayes pkgver=3.2.7 pkgrel=4 provides=("mrbayes") -pkgdesc="A program for the Bayesian estimation of phylogeny. doi:10.1093/sysbio/sys029" +pkgdesc="A program for the Bayesian estimation of phylogeny. https://doi.org/10.1093/sysbio/sys029" arch=('i686' 'x86_64') license=('GPL') url="http://nbisweden.github.io/MrBayes/" diff --git a/BioArchLinux/muscle/PKGBUILD b/BioArchLinux/muscle/PKGBUILD index f3aa5b8113..1ce9c750f3 100644 --- a/BioArchLinux/muscle/PKGBUILD +++ b/BioArchLinux/muscle/PKGBUILD @@ -4,7 +4,7 @@ pkgname=muscle pkgver=5.0.1428 pkgrel=5 -pkgdesc="Multiple sequence alignment software enabling improved estimates of phylogenetic tree confidence by ensemble bootstrapping. doi:10.1101/2021.06.20.449169" +pkgdesc="Multiple sequence alignment software enabling improved estimates of phylogenetic tree confidence by ensemble bootstrapping. https://doi.org/10.1101/2021.06.20.449169" arch=('i686' 'x86_64') url="http://www.drive5.com/muscle/" license=('GPL3') diff --git a/BioArchLinux/paml/PKGBUILD b/BioArchLinux/paml/PKGBUILD index b7861f697a..90a92ddac8 100644 --- a/BioArchLinux/paml/PKGBUILD +++ b/BioArchLinux/paml/PKGBUILD @@ -2,7 +2,7 @@ pkgname=paml pkgver=4.10.1 pkgrel=2 -pkgdesc="Phylogenetic analysis by maximum likelihood. doi:10.1093/molbev/msm088" +pkgdesc="Phylogenetic analysis by maximum likelihood. https://doi.org/10.1093/molbev/msm088" arch=('x86_64') url="http://abacus.gene.ucl.ac.uk/software/" license=('GPL3') diff --git a/BioArchLinux/paup/PKGBUILD b/BioArchLinux/paup/PKGBUILD index 31f4a0ac65..911c81a19b 100644 --- a/BioArchLinux/paup/PKGBUILD +++ b/BioArchLinux/paup/PKGBUILD @@ -4,7 +4,7 @@ pkgname=paup pkgver=4a168 _execname=paup${pkgver//.0/}_ubuntu64 pkgrel=4 -pkgdesc="Phylogenetic Analysis Using PAUP. doi:10.1002/0471250953.bi0604s00" +pkgdesc="Phylogenetic Analysis Using PAUP. https://doi.org/10.1002/0471250953.bi0604s00" arch=('i686' 'x86_64') url="http://phylosolutions.com/paup-test/" license=('custom') diff --git a/BioArchLinux/phylip/PKGBUILD b/BioArchLinux/phylip/PKGBUILD index 12d555131d..d53f0e117c 100644 --- a/BioArchLinux/phylip/PKGBUILD +++ b/BioArchLinux/phylip/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phylip pkgver=3.698 pkgrel=4 -pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies. doi:10.1111/j.1096-0031.1989.tb00562.x" +pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies. https://doi.org/10.1111/j.1096-0031.1989.tb00562.x" arch=('i686' 'x86_64') url="http://evolution.genetics.washington.edu/phylip.html" source=(http://evolution.gs.washington.edu/phylip/download/phylip-$pkgver.zip diff --git a/BioArchLinux/phylobayes-mpi/PKGBUILD b/BioArchLinux/phylobayes-mpi/PKGBUILD index 47b4372c87..fd1102004b 100644 --- a/BioArchLinux/phylobayes-mpi/PKGBUILD +++ b/BioArchLinux/phylobayes-mpi/PKGBUILD @@ -4,7 +4,7 @@ _pkgname=phylobayes pkgname=$_pkgname-mpi pkgver=1.8c pkgrel=4 -pkgdesc="phylogenetic reconstruction using infinite mixtures. doi:10.1093/molbev/msh112" +pkgdesc="phylogenetic reconstruction using infinite mixtures. https://doi.org/10.1093/molbev/msh112" arch=('i686' 'x86_64') url="https://github.com/bayesiancook/pbmpi" license=('GPL2') diff --git a/BioArchLinux/phylobayes/PKGBUILD b/BioArchLinux/phylobayes/PKGBUILD index 6ab0748e35..eda5183da1 100644 --- a/BioArchLinux/phylobayes/PKGBUILD +++ b/BioArchLinux/phylobayes/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phylobayes pkgver=4.1c pkgrel=3 -pkgdesc="phylogenetic reconstruction using infinite mixtures. doi:10.1093/molbev/msh112" +pkgdesc="phylogenetic reconstruction using infinite mixtures. https://doi.org/10.1093/molbev/msh112" arch=('i686' 'x86_64') url="https://github.com/bayesiancook/phylobayes" license=('unknow') diff --git a/BioArchLinux/phylonet-hmm/PKGBUILD b/BioArchLinux/phylonet-hmm/PKGBUILD index 5352795f56..b27d6616d1 100644 --- a/BioArchLinux/phylonet-hmm/PKGBUILD +++ b/BioArchLinux/phylonet-hmm/PKGBUILD @@ -9,7 +9,7 @@ depends=( 'java-runtime' ) makedepends=('ant') -pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes. doi:10.1371/journal.pcbi.1003649" +pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes. https://doi.org/10.1371/journal.pcbi.1003649" arch=('x86_64') url="https://bioinfocs.rice.edu/node/108" license=('GPL') diff --git a/BioArchLinux/phylonet/PKGBUILD b/BioArchLinux/phylonet/PKGBUILD index 4e0be16efc..cb6da35149 100644 --- a/BioArchLinux/phylonet/PKGBUILD +++ b/BioArchLinux/phylonet/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="TA suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events. doi:10.1093/sysbio/syy015" +pkgdesc="TA suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events. https://doi.org/10.1093/sysbio/syy015" arch=('x86_64') url="https://bioinfocs.rice.edu/PhyloNet" license=('GPL2') diff --git a/BioArchLinux/phylonium/PKGBUILD b/BioArchLinux/phylonium/PKGBUILD index 86aa79b6da..0e287c2a4a 100644 --- a/BioArchLinux/phylonium/PKGBUILD +++ b/BioArchLinux/phylonium/PKGBUILD @@ -2,7 +2,7 @@ pkgname=phylonium pkgver=1.6 pkgrel=1 -pkgdesc="Fast and Accurate Estimation of Evolutionary Distances. doi:10.1093/bioinformatics/btz903" +pkgdesc="Fast and Accurate Estimation of Evolutionary Distances. https://doi.org/10.1093/bioinformatics/btz903" url="https://github.com/evolbioinf/phylonium/" license=("GPL3") # "custom:ISC" depends=("libdivsufsort") diff --git a/BioArchLinux/phylosuite/PKGBUILD b/BioArchLinux/phylosuite/PKGBUILD index 0cfda2f415..a65525a653 100644 --- a/BioArchLinux/phylosuite/PKGBUILD +++ b/BioArchLinux/phylosuite/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phylosuite pkgver=1.2.2 pkgrel=4 -pkgdesc="an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. doi:10.1111/1755-0998.13096" +pkgdesc="an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. https://doi.org/10.1111/1755-0998.13096" arch=('x86_64') url="https://github.com/dongzhang0725/PhyloSuite" license=('GPL3') diff --git a/BioArchLinux/phyml/PKGBUILD b/BioArchLinux/phyml/PKGBUILD index 2295f48b96..cc4d45bd45 100644 --- a/BioArchLinux/phyml/PKGBUILD +++ b/BioArchLinux/phyml/PKGBUILD @@ -4,7 +4,7 @@ pkgname=phyml pkgver=3.3.20211231 pkgrel=1 epoch=1 -pkgdesc="Builds phylogenies from DNA or protein sequences using a maximum likelihood approach. doi:10.1093/sysbio/syq010" +pkgdesc="Builds phylogenies from DNA or protein sequences using a maximum likelihood approach. https://doi.org/10.1093/sysbio/syq010" arch=('i686' 'x86_64') url="https://github.com/stephaneguindon/phyml" license=('GPL2') diff --git a/BioArchLinux/pibuss/PKGBUILD b/BioArchLinux/pibuss/PKGBUILD index 920386c03f..ac4843ac28 100644 --- a/BioArchLinux/pibuss/PKGBUILD +++ b/BioArchLinux/pibuss/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. doi:10.1186/1471-2105-15-133" +pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133" arch=('x86_64') url="https://rega.kuleuven.be/cev/ecv/software/pibuss" license=('custom') diff --git a/BioArchLinux/popart/PKGBUILD b/BioArchLinux/popart/PKGBUILD index 1e3c6e97c6..d1d9e38270 100644 --- a/BioArchLinux/popart/PKGBUILD +++ b/BioArchLinux/popart/PKGBUILD @@ -3,7 +3,7 @@ pkgname=popart pkgver=20190715.150937 pkgrel=3 -pkgdesc="Full-feature software for haplotype network reconstruction. doi:10.1111/2041-210X.12410" +pkgdesc="Full-feature software for haplotype network reconstruction. https://doi.org/10.1111/2041-210X.12410" arch=('x86_64') url="http://popart.otago.ac.nz/index.shtml" license=('LGPLv2') diff --git a/BioArchLinux/primer3/PKGBUILD b/BioArchLinux/primer3/PKGBUILD index d3a9cf1cf5..73b5fceaf8 100644 --- a/BioArchLinux/primer3/PKGBUILD +++ b/BioArchLinux/primer3/PKGBUILD @@ -3,7 +3,7 @@ pkgname=primer3 pkgver=2.5.0 pkgrel=4 -pkgdesc="Tool to design flanking oligo nucleotides for DNA amplification. doi:10.1093/nar/gks596" +pkgdesc="Tool to design flanking oligo nucleotides for DNA amplification. https://doi.org/10.1093/nar/gks596" arch=('i686' 'x86_64') license=('GPL2') depends=('gcc-libs') diff --git a/BioArchLinux/rasp/PKGBUILD b/BioArchLinux/rasp/PKGBUILD index b98450d74e..f7812542da 100644 --- a/BioArchLinux/rasp/PKGBUILD +++ b/BioArchLinux/rasp/PKGBUILD @@ -4,7 +4,7 @@ pkgname=rasp pkgver=20211014 pkgrel=4 -pkgdesc="Ancestral state reconstruction tool for multiple genes and characters. doi:10.1093/molbev/msz257" +pkgdesc="Ancestral state reconstruction tool for multiple genes and characters. https://doi.org/10.1093/molbev/msz257" arch=('x86_64') url="http://mnh.scu.edu.cn/soft/blog/rasp/" license=('GPL3') diff --git a/BioArchLinux/raxml-mpi/PKGBUILD b/BioArchLinux/raxml-mpi/PKGBUILD index 70e6dda0d3..f238bf5717 100644 --- a/BioArchLinux/raxml-mpi/PKGBUILD +++ b/BioArchLinux/raxml-mpi/PKGBUILD @@ -4,7 +4,7 @@ pkgname=raxml-mpi pkgver=8.2.12 pkgrel=4 -pkgdesc="Randomized Axelerated Maximum Likelihood. doi:10.1093/bioinformatics/btu033" +pkgdesc="Randomized Axelerated Maximum Likelihood. https://doi.org/10.1093/bioinformatics/btu033" arch=('x86_64') url="http://sco.h-its.org/exelixis/web/software/raxml/" license=('GPL3') diff --git a/BioArchLinux/raxml-ng-mpi/PKGBUILD b/BioArchLinux/raxml-ng-mpi/PKGBUILD index 8870f82f33..fca7017efd 100644 --- a/BioArchLinux/raxml-ng-mpi/PKGBUILD +++ b/BioArchLinux/raxml-ng-mpi/PKGBUILD @@ -6,7 +6,7 @@ pkgname=raxml-ng-mpi pkgver=1.1.0 _commit=411611611793e53c992717d869ca64370f2e4789 pkgrel=17 -pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. doi:10.1093/bioinformatics/btz305" +pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. https://doi.org/10.1093/bioinformatics/btz305" url='https://github.com/amkozlov/raxml-ng' arch=('x86_64') license=('AGPL3') diff --git a/BioArchLinux/raxml-ng/PKGBUILD b/BioArchLinux/raxml-ng/PKGBUILD index 9fec3bfad8..d52edf3e79 100644 --- a/BioArchLinux/raxml-ng/PKGBUILD +++ b/BioArchLinux/raxml-ng/PKGBUILD @@ -5,7 +5,7 @@ pkgname=raxml-ng pkgver=1.1.0 _commit=411611611793e53c992717d869ca64370f2e4789 pkgrel=16 -pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. doi:10.1093/bioinformatics/btz305" +pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. https://doi.org/10.1093/bioinformatics/btz305" url='https://github.com/amkozlov/raxml-ng' arch=('x86_64') license=('AGPL3') diff --git a/BioArchLinux/raxml/PKGBUILD b/BioArchLinux/raxml/PKGBUILD index 32f76ad7a3..6cc6ff7d7b 100644 --- a/BioArchLinux/raxml/PKGBUILD +++ b/BioArchLinux/raxml/PKGBUILD @@ -3,7 +3,7 @@ pkgname=raxml pkgver=8.2.12 pkgrel=4 -pkgdesc="Randomized Axelerated Maximum Likelihood. doi:10.1093/bioinformatics/btu033" +pkgdesc="Randomized Axelerated Maximum Likelihood. https://doi.org/10.1093/bioinformatics/btu033" arch=('x86_64') url="http://sco.h-its.org/exelixis/web/software/raxml/" license=('GPL3') diff --git a/BioArchLinux/raxmlgui/PKGBUILD b/BioArchLinux/raxmlgui/PKGBUILD index 8f60eeec0d..a7b1239dd4 100644 --- a/BioArchLinux/raxmlgui/PKGBUILD +++ b/BioArchLinux/raxmlgui/PKGBUILD @@ -4,7 +4,7 @@ pkgname=raxmlgui pkgver=2.0.6 pkgrel=2 -pkgdesc="A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis. doi:10.1111/2041-210X.13512" +pkgdesc="A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis. https://doi.org/10.1111/2041-210X.13512" arch=('x86_64') url="https://antonellilab.github.io/raxmlGUI" provides=("raxmlgui") diff --git a/BioArchLinux/samtools/PKGBUILD b/BioArchLinux/samtools/PKGBUILD index 4c4ff427fd..c732bc9cc8 100644 --- a/BioArchLinux/samtools/PKGBUILD +++ b/BioArchLinux/samtools/PKGBUILD @@ -7,7 +7,7 @@ pkgname=samtools pkgver=1.14 pkgrel=4 -pkgdesc="tools for manipulating next-generation sequencing data. doi:10.1093/bioinformatics/btp352" +pkgdesc="tools for manipulating next-generation sequencing data. https://doi.org/10.1093/bioinformatics/btp352" arch=('i686' 'x86_64') url="http://www.htslib.org/" license=('custom') diff --git a/BioArchLinux/seaview/PKGBUILD b/BioArchLinux/seaview/PKGBUILD index 67538e2506..3535fccf66 100644 --- a/BioArchLinux/seaview/PKGBUILD +++ b/BioArchLinux/seaview/PKGBUILD @@ -4,7 +4,7 @@ pkgname=seaview pkgver=5.0.5 pkgrel=3 -pkgdesc="GUI for multiple sequence alignment and molecular phylogeny. doi:10.1093/molbev/msp259" +pkgdesc="GUI for multiple sequence alignment and molecular phylogeny. https://doi.org/10.1093/molbev/msp259" arch=('x86_64') url="http://doua.prabi.fr/software/seaview" license=('GPL3') diff --git a/BioArchLinux/seqan/PKGBUILD b/BioArchLinux/seqan/PKGBUILD index 489191bc92..ff176ac614 100644 --- a/BioArchLinux/seqan/PKGBUILD +++ b/BioArchLinux/seqan/PKGBUILD @@ -1,7 +1,7 @@ pkgname=seqan pkgver=2.4.0 pkgrel=4 -pkgdesc="SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. doi:10.1186/1471-2105-9-11" +pkgdesc="SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. https://doi.org/10.1186/1471-2105-9-11" arch=("any") url="http://www.seqan.de" license=('custom') diff --git a/BioArchLinux/seqan3/PKGBUILD b/BioArchLinux/seqan3/PKGBUILD index eac77d1518..de3c8d7ea5 100644 --- a/BioArchLinux/seqan3/PKGBUILD +++ b/BioArchLinux/seqan3/PKGBUILD @@ -1,7 +1,7 @@ pkgname=seqan3 pkgver=3.1.0 pkgrel=4 -pkgdesc="The modern C++ library for sequence analysis. Contains version 3 of the library and API docs. doi:10.1016/j.jbiotec.2017.07.017" +pkgdesc="The modern C++ library for sequence analysis. Contains version 3 of the library and API docs. https://doi.org/10.1016/j.jbiotec.2017.07.017" arch=("any") url="http://www.seqan.de" license=('custom') diff --git a/BioArchLinux/spread/PKGBUILD b/BioArchLinux/spread/PKGBUILD index 91b0e8ee39..946321b130 100644 --- a/BioArchLinux/spread/PKGBUILD +++ b/BioArchLinux/spread/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion. doi:10.1093/bioinformatics/btr481" +pkgdesc="a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion. https://doi.org/10.1093/bioinformatics/btr481" arch=('x86_64') url="https://rega.kuleuven.be/cev/ecv/software/${pkgname}" license=('custom') diff --git a/BioArchLinux/spread3/PKGBUILD b/BioArchLinux/spread3/PKGBUILD index d4d14737d8..eb1a9ebd52 100644 --- a/BioArchLinux/spread3/PKGBUILD +++ b/BioArchLinux/spread3/PKGBUILD @@ -8,7 +8,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes. doi:10.1093/molbev/msw082" +pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes. https://doi.org/10.1093/molbev/msw082" arch=('x86_64') url="https://rega.kuleuven.be/cev/ecv/software/SpreaD3" license=('custom') diff --git a/BioArchLinux/tempest/PKGBUILD b/BioArchLinux/tempest/PKGBUILD index 83e68b4636..b714d1e3d1 100644 --- a/BioArchLinux/tempest/PKGBUILD +++ b/BioArchLinux/tempest/PKGBUILD @@ -7,7 +7,7 @@ pkgrel=4 depends=( 'java-runtime' ) -pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. doi:10.1093/ve/vew007" +pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. https://doi.org/10.1093/ve/vew007" arch=('x86_64') url="http://tree.bio.ed.ac.uk/software/tempest/" license=('GPL2') diff --git a/BioArchLinux/tiger/PKGBUILD b/BioArchLinux/tiger/PKGBUILD index 9b5521ce10..97fe6bb5d1 100644 --- a/BioArchLinux/tiger/PKGBUILD +++ b/BioArchLinux/tiger/PKGBUILD @@ -4,7 +4,7 @@ pkgname=tiger pkgver=1.02 pkgrel=4 -pkgdesc="Identifying rapidly-evolving characters in evolutionary data. doi:10.1093/sysbio/syr064" +pkgdesc="Identifying rapidly-evolving characters in evolutionary data. https://doi.org/10.1093/sysbio/syr064" arch=('x86_64') url="http://mcinerneylab.com/software/tiger/","" license=('GPL3') diff --git a/BioArchLinux/tnt-gui/PKGBUILD b/BioArchLinux/tnt-gui/PKGBUILD index 10d88a045d..fcd8b06a3d 100644 --- a/BioArchLinux/tnt-gui/PKGBUILD +++ b/BioArchLinux/tnt-gui/PKGBUILD @@ -4,7 +4,7 @@ pkgname=tnt-gui pkgver=2021.12.27 pkgrel=1 -pkgdesc="Tree analysis using New Technology. doi:10.1111/cla.12160" +pkgdesc="Tree analysis using New Technology. https://doi.org/10.1111/cla.12160" arch=('x86_64') url="http://www.lillo.org.ar/phylogeny/tnt/" license=('custom') diff --git a/BioArchLinux/tnt-mpi/PKGBUILD b/BioArchLinux/tnt-mpi/PKGBUILD index 6f8f87572a..4de33d02f0 100644 --- a/BioArchLinux/tnt-mpi/PKGBUILD +++ b/BioArchLinux/tnt-mpi/PKGBUILD @@ -5,7 +5,7 @@ pkgname=tnt-mpi _pkgname=mpitnt pkgver=2021.12.27 pkgrel=1 -pkgdesc="Tree analysis using New Technology. doi:10.1111/cla.12160" +pkgdesc="Tree analysis using New Technology. https://doi.org/10.1111/cla.12160" arch=('x86_64') url="http://www.lillo.org.ar/phylogeny/tnt/" provides=('tnt') diff --git a/BioArchLinux/tnt/PKGBUILD b/BioArchLinux/tnt/PKGBUILD index e573ecbe2c..51061d4499 100644 --- a/BioArchLinux/tnt/PKGBUILD +++ b/BioArchLinux/tnt/PKGBUILD @@ -4,7 +4,7 @@ pkgname=tnt pkgver=2021.12.27 pkgrel=1 -pkgdesc="Tree analysis using New Technology. doi:10.1111/cla.12160" +pkgdesc="Tree analysis using New Technology. https://doi.org/10.1111/cla.12160" arch=('x86_64') url="http://www.lillo.org.ar/phylogeny/tnt/" provides=('tnt') diff --git a/BioArchLinux/tracer/PKGBUILD b/BioArchLinux/tracer/PKGBUILD index e6025f7114..c243008f48 100644 --- a/BioArchLinux/tracer/PKGBUILD +++ b/BioArchLinux/tracer/PKGBUILD @@ -5,7 +5,7 @@ pkgname=tracer _pkgname=Tracer pkgver=1.7.2 pkgrel=3 -pkgdesc="Posterior summarisation in Bayesian phylogenetics. doi:10.1093/sysbio/syy032" +pkgdesc="Posterior summarisation in Bayesian phylogenetics. https://doi.org/10.1093/sysbio/syy032" arch=('x86_64') url="https://github.com/beast-dev/tracer" license=('unknown') diff --git a/BioArchLinux/tracy/PKGBUILD b/BioArchLinux/tracy/PKGBUILD index 3ebc616441..4e1478ac55 100644 --- a/BioArchLinux/tracy/PKGBUILD +++ b/BioArchLinux/tracy/PKGBUILD @@ -3,7 +3,7 @@ pkgname=tracy pkgver=0.6.1 pkgrel=4 -pkgdesc="Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files. doi:10.1186/s12864-020-6635-8" +pkgdesc="Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files. https://doi.org/10.1186/s12864-020-6635-8" arch=('x86_64') url="https://github.com/gear-genomics/tracy" license=('BSDv3') diff --git a/BioArchLinux/trimal/PKGBUILD b/BioArchLinux/trimal/PKGBUILD index dd542f4e00..be6f833de7 100644 --- a/BioArchLinux/trimal/PKGBUILD +++ b/BioArchLinux/trimal/PKGBUILD @@ -2,7 +2,7 @@ pkgname=trimal pkgver=1.4.1 pkgrel=6 -pkgdesc="A tool for automated alignment trimming in large-scale phylogenetic analyses. doi:10.1093/bioinformatics/btp348" +pkgdesc="A tool for automated alignment trimming in large-scale phylogenetic analyses. https://doi.org/10.1093/bioinformatics/btp348" arch=('x86_64') url="trimal.cgenomics.org" license=('GPL') diff --git a/BioArchLinux/ugene/PKGBUILD b/BioArchLinux/ugene/PKGBUILD index 3ddf8fa38c..de90b8d58e 100644 --- a/BioArchLinux/ugene/PKGBUILD +++ b/BioArchLinux/ugene/PKGBUILD @@ -4,7 +4,7 @@ pkgname=ugene pkgver=41.0 pkgrel=3 -pkgdesc="A free cross-platform genome analysis suite. doi:10.1093/bioinformatics/bts091" +pkgdesc="A free cross-platform genome analysis suite. https://doi.org/10.1093/bioinformatics/bts091" arch=('x86_64') url="http://ugene.net" license=('GPL') diff --git a/BioArchLinux/vcftools/PKGBUILD b/BioArchLinux/vcftools/PKGBUILD index 246a54e4f0..e24d9569ce 100644 --- a/BioArchLinux/vcftools/PKGBUILD +++ b/BioArchLinux/vcftools/PKGBUILD @@ -4,7 +4,7 @@ pkgname=vcftools pkgver=0.1.16 pkgrel=4 -pkgdesc="A set of tools written in Perl and C++ for working with VCF files. doi:10.1093/bioinformatics/btr330" +pkgdesc="A set of tools written in Perl and C++ for working with VCF files. https://doi.org/10.1093/bioinformatics/btr330" arch=('x86_64') url="https://vcftools.github.io/" license=('LGPL3') From 36fd5f6afcaabf90654b80983198d02688f49864 Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Mon, 3 Jan 2022 23:20:01 +0100 Subject: [PATCH 06/10] Fixed bad DOI for hmmer --- BioArchLinux/hmmer/PKGBUILD | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/BioArchLinux/hmmer/PKGBUILD b/BioArchLinux/hmmer/PKGBUILD index 72098a83b1..900f908549 100644 --- a/BioArchLinux/hmmer/PKGBUILD +++ b/BioArchLinux/hmmer/PKGBUILD @@ -5,7 +5,7 @@ pkgname=hmmer pkgver=3.3.2 pkgrel=1 -pkgdesc="Profile hidden Markov models (HMMs) for database searching using consensus sequences. dio:10.1093/bioinformatics/14.9.755" +pkgdesc="Profile hidden Markov models (HMMs) for database searching using consensus sequences. https://doi.org/10.1093/bioinformatics/14.9.755" arch=('i686' 'x86_64') checkdepends=('perl-perl4-corelibs' 'python') license=('GPL') From 699d7dad66ab21e7dcb9b8910c6cddaec330cfd5 Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Tue, 4 Jan 2022 00:17:38 +0100 Subject: [PATCH 07/10] Add mummer4 --- BioArchLinux/mummer4/PKGBUILD | 25 +++++++++++++++++++++++++ BioArchLinux/mummer4/lilac.py | 11 +++++++++++ BioArchLinux/mummer4/lilac.yaml | 10 ++++++++++ 3 files changed, 46 insertions(+) create mode 100644 BioArchLinux/mummer4/PKGBUILD create mode 100644 BioArchLinux/mummer4/lilac.py create mode 100644 BioArchLinux/mummer4/lilac.yaml diff --git a/BioArchLinux/mummer4/PKGBUILD b/BioArchLinux/mummer4/PKGBUILD new file mode 100644 index 0000000000..3562084682 --- /dev/null +++ b/BioArchLinux/mummer4/PKGBUILD @@ -0,0 +1,25 @@ +# Maintainer: Mick Elliot +# Contributor: Mick Elliot + +pkgname=mummer4 +pkgver=4.0.0rc1 +pkgrel=1 +pkgdesc="A fast and versatile genome alignment system. https://doi.org/10.1371/journal.pcbi.1005944" +arch=('x86_64') +url="https://mummer4.github.io/" +license=('MIT') +depends=() +provides=() +source=("https://github.com/${pkgname}/mummer/releases/download/v${pkgver}/mummer-${pkgver}.tar.gz") +sha256sums=('85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d') + +build() { + cd "mummer-${pkgver}" + ./configure --prefix=/usr + make +} + +package() { + cd "mummer-${pkgver}" + make DESTDIR="$pkgdir/" install +} diff --git a/BioArchLinux/mummer4/lilac.py b/BioArchLinux/mummer4/lilac.py new file mode 100644 index 0000000000..e3ec09df9a --- /dev/null +++ b/BioArchLinux/mummer4/lilac.py @@ -0,0 +1,11 @@ +#!/usr/bin/env python3 + +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() + diff --git a/BioArchLinux/mummer4/lilac.yaml b/BioArchLinux/mummer4/lilac.yaml new file mode 100644 index 0000000000..98b54ff6bd --- /dev/null +++ b/BioArchLinux/mummer4/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: + - github: michaelgelliot + email: m.g.elliot@rug.nl +update_on: + - source: github + github: mummer4/mummer + use_max_tag: true + + From 6b200c15785285a2edd63ead31491bc73989aaa7 Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Tue, 4 Jan 2022 00:54:23 +0100 Subject: [PATCH 08/10] fixed dependencies and license for mummer4 --- BioArchLinux/mummer4/PKGBUILD | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/BioArchLinux/mummer4/PKGBUILD b/BioArchLinux/mummer4/PKGBUILD index 3562084682..41f6911a94 100644 --- a/BioArchLinux/mummer4/PKGBUILD +++ b/BioArchLinux/mummer4/PKGBUILD @@ -7,8 +7,9 @@ pkgrel=1 pkgdesc="A fast and versatile genome alignment system. https://doi.org/10.1371/journal.pcbi.1005944" arch=('x86_64') url="https://mummer4.github.io/" -license=('MIT') -depends=() +license=('GPL' 'PerlArtistic') +depends=(gcc-libs) +makedepends=(sh perl) provides=() source=("https://github.com/${pkgname}/mummer/releases/download/v${pkgver}/mummer-${pkgver}.tar.gz") sha256sums=('85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d') From c0624f38c85e7f98aba89f9b318da1596c402848 Mon Sep 17 00:00:00 2001 From: Mick Elliot Date: Tue, 4 Jan 2022 02:21:14 +0100 Subject: [PATCH 09/10] Added test suite to mummer but commented out due to apparent bug --- BioArchLinux/mummer4/PKGBUILD | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/BioArchLinux/mummer4/PKGBUILD b/BioArchLinux/mummer4/PKGBUILD index 41f6911a94..4b8be47a28 100644 --- a/BioArchLinux/mummer4/PKGBUILD +++ b/BioArchLinux/mummer4/PKGBUILD @@ -7,7 +7,7 @@ pkgrel=1 pkgdesc="A fast and versatile genome alignment system. https://doi.org/10.1371/journal.pcbi.1005944" arch=('x86_64') url="https://mummer4.github.io/" -license=('GPL' 'PerlArtistic') +license=('PerlArtistic') depends=(gcc-libs) makedepends=(sh perl) provides=() @@ -20,7 +20,16 @@ build() { make } +# check seems to fail due to an apparent bug in test_md5 +# see also https://github.com/mummer4/mummer/issues/147 + +# check() { +# cd "mummer-${pkgver}" +# make check +# } + package() { cd "mummer-${pkgver}" make DESTDIR="$pkgdir/" install } + From 248e45905442757a8c99d4ee4739fd9742a01bbd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E6=9C=88=E5=AD=A3=E8=8A=B1=E4=B8=AD=E7=9A=84=E6=98=9F?= =?UTF-8?q?=E8=BE=B0?= Date: Tue, 4 Jan 2022 06:24:57 +0000 Subject: [PATCH 10/10] try to promote it the writing of the tag does not follow some rules, so I try to use regex to try --- BioArchLinux/mummer4/lilac.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/BioArchLinux/mummer4/lilac.yaml b/BioArchLinux/mummer4/lilac.yaml index 98b54ff6bd..f6d2350b77 100644 --- a/BioArchLinux/mummer4/lilac.yaml +++ b/BioArchLinux/mummer4/lilac.yaml @@ -3,8 +3,8 @@ maintainers: - github: michaelgelliot email: m.g.elliot@rug.nl update_on: - - source: github - github: mummer4/mummer - use_max_tag: true + - source: regex + regex: v(\d+.\d+.\w+) + url: https://github.com/mummer4/mummer/releases