diff --git a/BioArchLinux/shapeit4/PKGBUILD b/BioArchLinux/shapeit4/PKGBUILD new file mode 100644 index 0000000000..09360d7a7f --- /dev/null +++ b/BioArchLinux/shapeit4/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Ramiro Magno +pkgname=shapeit4 +pkgver=4.2.2 +pkgrel=2 +pkgdesc="Segmented HAPlotype Estimation and Imputation Tools" +arch=('i686' 'x86_64') +url="https://odelaneau.github.io/shapeit4/" +license=('MIT') +depends=('zlib' 'bzip2' 'xz' 'glibc') +makedepends=('boost' 'htslib' 'gcc') +source=("${pkgname}-${pkgver}.tar.gz"::"https://github.com/odelaneau/${pkgname}/archive/refs/tags/v${pkgver}.tar.gz" "shapeit4.patch") +noextract=() +sha256sums=("9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556" "b380dfeac4a28af4877d5f3f534864bd4c5090ed59f27c4da36c40bd18448457") +validpgpkeys=() + +prepare() { + patch -p0 -i "shapeit4.patch" +} + +build() { + cd "$pkgname-$pkgver" + make +} + +package() { + cd "$pkgname-$pkgver" + + # Binaries + install -Dm755 bin/shapeit4.2 "${pkgdir}/usr/bin/shapeit4" + install -Dm755 tools/bingraphsample/bin/bingraphsample "${pkgdir}/usr/bin/bingraphsample" + + # Example data + mkdir -p "${pkgdir}/usr/share/${pkgname}" + install -Dm644 test/*.gmap.gz "${pkgdir}/usr/share/${pkgname}/" + install -Dm644 test/*.vcf.gz "${pkgdir}/usr/share/${pkgname}/" + install -Dm644 test/*.vcf.gz.csi "${pkgdir}/usr/share/${pkgname}/" + install -Dm644 test/*.bcf "${pkgdir}/usr/share/${pkgname}/" + install -Dm644 test/*.bcf.csi "${pkgdir}/usr/share/${pkgname}/" +} + diff --git a/BioArchLinux/shapeit4/lilac.py b/BioArchLinux/shapeit4/lilac.py new file mode 100644 index 0000000000..8a6e65aeba --- /dev/null +++ b/BioArchLinux/shapeit4/lilac.py @@ -0,0 +1,11 @@ +#!/usr/bin/env python3 + +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/shapeit4/lilac.yaml b/BioArchLinux/shapeit4/lilac.yaml new file mode 100644 index 0000000000..750a0fc1d1 --- /dev/null +++ b/BioArchLinux/shapeit4/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: + - github: starsareintherose + email: kuoi@bioarchlinux.org +update_on: + - source: github + github: odelaneau/shapeit4 + use_max_tag: true + prefix: 'v' + - alias: alpm-lilac + alpm: htslib + strip_release: true +repo_depends: + - htslib diff --git a/BioArchLinux/shapeit4/shapeit4.patch b/BioArchLinux/shapeit4/shapeit4.patch new file mode 100644 index 0000000000..772d27ebd0 --- /dev/null +++ b/BioArchLinux/shapeit4/shapeit4.patch @@ -0,0 +1,95 @@ +diff '--color=auto' -ur shapeit4-4.2.2/makefile shapeit4-4.2.2-1/makefile +--- shapeit4-4.2.2/makefile 2021-09-07 13:08:23.000000000 +0100 ++++ shapeit4-4.2.2-1/makefile 2022-05-23 10:02:02.950631934 +0100 +@@ -2,22 +2,13 @@ + CXX=g++ -std=c++11 + + #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] +-HTSLIB_INC=$(HOME)/Tools/htslib-1.11 +-HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a ++HTSLIB_INC=/usr/include/htslib ++HTSLIB_LIB=/usr/lib/libhts.a + + #BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS] +-BOOST_INC=/usr/include +-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a +-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a +- +-#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] +-#HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include +-#HTSLIB_LIB=/software/UHTS/Analysis/samtools/1.4/lib64/libhts.a +- +-#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS] +-#BOOST_INC=/software/include +-#BOOST_LIB_IO=/software/lib64/libboost_iostreams.a +-#BOOST_LIB_PO=/software/lib64/libboost_program_options.a ++BOOST_INC=/usr/include/boost ++BOOST_LIB_IO=/usr/lib/libboost_iostreams.a ++BOOST_LIB_PO=/usr/lib/libboost_program_options.a + + #COMPILER & LINKER FLAGS + +@@ -32,9 +23,8 @@ + + LDFLAG=-O3 + +- + #DYNAMIC LIBRARIES +-DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto ++DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto -ldl + + #SHAPEIT SOURCES & BINARY + BFILE=bin/shapeit4.2 +Binary files shapeit4-4.2.2/tools/bingraphsample/bin/bingraphsample and shapeit4-4.2.2-1/tools/bingraphsample/bin/bingraphsample differ +diff '--color=auto' -ur shapeit4-4.2.2/tools/bingraphsample/makefile shapeit4-4.2.2-1/tools/bingraphsample/makefile +--- shapeit4-4.2.2/tools/bingraphsample/makefile 2021-09-07 13:08:23.000000000 +0100 ++++ shapeit4-4.2.2-1/tools/bingraphsample/makefile 2022-05-23 10:08:28.457309881 +0100 +@@ -2,22 +2,13 @@ + CXX=g++ -std=c++11 + + #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] +-HTSLIB_INC=$(HOME)/Tools/htslib-1.9 +-HTSLIB_LIB=$(HOME)/Tools/htslib-1.9/libhts.a ++HTSLIB_INC=/usr/include/htslib ++HTSLIB_LIB=/usr/lib/libhts.a + + #BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS] +-BOOST_INC=/usr/include +-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a +-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a +- +-#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] +-#HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include +-#HTSLIB_LIB=/software/UHTS/Analysis/samtools/1.4/lib64/libhts.a +- +-#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS] +-#BOOST_INC=/software/include +-#BOOST_LIB_IO=/software/lib64/libboost_iostreams.a +-#BOOST_LIB_PO=/software/lib64/libboost_program_options.a ++BOOST_INC=/usr/include/boost ++BOOST_LIB_IO=/usr/lib/libboost_iostreams.a ++BOOST_LIB_PO=/usr/lib/libboost_program_options.a + + #COMPILER & LINKER FLAGS + #Best performance is achieved with this. Use it if running on the same plateform you're compiling, it's definitely worth it! +@@ -29,7 +20,7 @@ + LDFLAG=-O3 + + #DYNAMIC LIBRARIES +-DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma ++DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -ldl + + #SHAPEIT SOURCES & BINARY + BFILE=bin/bingraphsample +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/genotype_managment.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/genotype_managment.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/genotype_set.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/genotype_set.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/genotype_sweep.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/genotype_sweep.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/graph_reader.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/graph_reader.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/haplotype_writer.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/haplotype_writer.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/main.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/main.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/sampler_finalise.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/sampler_finalise.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/sampler_initialise.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/sampler_initialise.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/sampler_management.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/sampler_management.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/sampler_parameters.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/sampler_parameters.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/variant_map.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/variant_map.o differ +Binary files shapeit4-4.2.2/tools/bingraphsample/obj/variant.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/variant.o differ