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shapeit4: init
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Kuoi
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4 changed files with 160 additions and 0 deletions
40
BioArchLinux/shapeit4/PKGBUILD
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40
BioArchLinux/shapeit4/PKGBUILD
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# Maintainer: Ramiro Magno <ramiro dot magno at gmail.com>
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pkgname=shapeit4
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pkgver=4.2.2
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pkgrel=2
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pkgdesc="Segmented HAPlotype Estimation and Imputation Tools"
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arch=('i686' 'x86_64')
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url="https://odelaneau.github.io/shapeit4/"
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license=('MIT')
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depends=('zlib' 'bzip2' 'xz' 'glibc')
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makedepends=('boost' 'htslib' 'gcc')
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source=("${pkgname}-${pkgver}.tar.gz"::"https://github.com/odelaneau/${pkgname}/archive/refs/tags/v${pkgver}.tar.gz" "shapeit4.patch")
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noextract=()
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sha256sums=("9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556" "b380dfeac4a28af4877d5f3f534864bd4c5090ed59f27c4da36c40bd18448457")
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validpgpkeys=()
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prepare() {
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patch -p0 -i "shapeit4.patch"
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}
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build() {
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cd "$pkgname-$pkgver"
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make
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}
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package() {
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cd "$pkgname-$pkgver"
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# Binaries
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install -Dm755 bin/shapeit4.2 "${pkgdir}/usr/bin/shapeit4"
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install -Dm755 tools/bingraphsample/bin/bingraphsample "${pkgdir}/usr/bin/bingraphsample"
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# Example data
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mkdir -p "${pkgdir}/usr/share/${pkgname}"
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install -Dm644 test/*.gmap.gz "${pkgdir}/usr/share/${pkgname}/"
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install -Dm644 test/*.vcf.gz "${pkgdir}/usr/share/${pkgname}/"
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install -Dm644 test/*.vcf.gz.csi "${pkgdir}/usr/share/${pkgname}/"
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install -Dm644 test/*.bcf "${pkgdir}/usr/share/${pkgname}/"
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install -Dm644 test/*.bcf.csi "${pkgdir}/usr/share/${pkgname}/"
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}
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11
BioArchLinux/shapeit4/lilac.py
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BioArchLinux/shapeit4/lilac.py
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#!/usr/bin/env python3
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from lilaclib import *
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def pre_build():
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update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
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run_cmd(['updpkgsums'])
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def post_build():
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git_add_files('PKGBUILD')
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git_commit()
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14
BioArchLinux/shapeit4/lilac.yaml
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BioArchLinux/shapeit4/lilac.yaml
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build_prefix: extra-x86_64
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maintainers:
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- github: starsareintherose
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email: kuoi@bioarchlinux.org
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update_on:
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- source: github
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github: odelaneau/shapeit4
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use_max_tag: true
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prefix: 'v'
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- alias: alpm-lilac
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alpm: htslib
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strip_release: true
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repo_depends:
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- htslib
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95
BioArchLinux/shapeit4/shapeit4.patch
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BioArchLinux/shapeit4/shapeit4.patch
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diff '--color=auto' -ur shapeit4-4.2.2/makefile shapeit4-4.2.2-1/makefile
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--- shapeit4-4.2.2/makefile 2021-09-07 13:08:23.000000000 +0100
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+++ shapeit4-4.2.2-1/makefile 2022-05-23 10:02:02.950631934 +0100
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@@ -2,22 +2,13 @@
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CXX=g++ -std=c++11
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#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
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-HTSLIB_INC=$(HOME)/Tools/htslib-1.11
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-HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a
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+HTSLIB_INC=/usr/include/htslib
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+HTSLIB_LIB=/usr/lib/libhts.a
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#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
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-BOOST_INC=/usr/include
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-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
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-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
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-
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-#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
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-#HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include
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-#HTSLIB_LIB=/software/UHTS/Analysis/samtools/1.4/lib64/libhts.a
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-
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-#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
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-#BOOST_INC=/software/include
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-#BOOST_LIB_IO=/software/lib64/libboost_iostreams.a
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-#BOOST_LIB_PO=/software/lib64/libboost_program_options.a
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+BOOST_INC=/usr/include/boost
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+BOOST_LIB_IO=/usr/lib/libboost_iostreams.a
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+BOOST_LIB_PO=/usr/lib/libboost_program_options.a
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#COMPILER & LINKER FLAGS
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@@ -32,9 +23,8 @@
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LDFLAG=-O3
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-
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#DYNAMIC LIBRARIES
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-DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto
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+DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto -ldl
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#SHAPEIT SOURCES & BINARY
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BFILE=bin/shapeit4.2
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Binary files shapeit4-4.2.2/tools/bingraphsample/bin/bingraphsample and shapeit4-4.2.2-1/tools/bingraphsample/bin/bingraphsample differ
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diff '--color=auto' -ur shapeit4-4.2.2/tools/bingraphsample/makefile shapeit4-4.2.2-1/tools/bingraphsample/makefile
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--- shapeit4-4.2.2/tools/bingraphsample/makefile 2021-09-07 13:08:23.000000000 +0100
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+++ shapeit4-4.2.2-1/tools/bingraphsample/makefile 2022-05-23 10:08:28.457309881 +0100
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@@ -2,22 +2,13 @@
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CXX=g++ -std=c++11
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#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
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-HTSLIB_INC=$(HOME)/Tools/htslib-1.9
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-HTSLIB_LIB=$(HOME)/Tools/htslib-1.9/libhts.a
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+HTSLIB_INC=/usr/include/htslib
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+HTSLIB_LIB=/usr/lib/libhts.a
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#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
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-BOOST_INC=/usr/include
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-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
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-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
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-
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-#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
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-#HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include
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-#HTSLIB_LIB=/software/UHTS/Analysis/samtools/1.4/lib64/libhts.a
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-
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-#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
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-#BOOST_INC=/software/include
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-#BOOST_LIB_IO=/software/lib64/libboost_iostreams.a
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-#BOOST_LIB_PO=/software/lib64/libboost_program_options.a
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+BOOST_INC=/usr/include/boost
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+BOOST_LIB_IO=/usr/lib/libboost_iostreams.a
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+BOOST_LIB_PO=/usr/lib/libboost_program_options.a
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#COMPILER & LINKER FLAGS
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#Best performance is achieved with this. Use it if running on the same plateform you're compiling, it's definitely worth it!
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@@ -29,7 +20,7 @@
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LDFLAG=-O3
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#DYNAMIC LIBRARIES
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-DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma
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+DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -ldl
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#SHAPEIT SOURCES & BINARY
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BFILE=bin/bingraphsample
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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
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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
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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
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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
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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
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Binary files shapeit4-4.2.2/tools/bingraphsample/obj/main.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/main.o differ
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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
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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
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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
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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
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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
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Binary files shapeit4-4.2.2/tools/bingraphsample/obj/variant.o and shapeit4-4.2.2-1/tools/bingraphsample/obj/variant.o differ
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