mirror of
https://github.com/BioArchLinux/Packages.git
synced 2025-03-10 12:02:42 +00:00
shapeit4: init
This commit is contained in:
Kuoi
parent
581cf5e461
commit
11d0952a35
4 changed files with 160 additions and 0 deletions
40
BioArchLinux/shapeit4/PKGBUILD
Normal file
40
BioArchLinux/shapeit4/PKGBUILD
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
# Maintainer: Ramiro Magno <ramiro dot magno at gmail.com>
|
||||
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}/"
|
||||
}
|
||||
|
||||
11
BioArchLinux/shapeit4/lilac.py
Normal file
11
BioArchLinux/shapeit4/lilac.py
Normal file
|
|
@ -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()
|
||||
14
BioArchLinux/shapeit4/lilac.yaml
Normal file
14
BioArchLinux/shapeit4/lilac.yaml
Normal file
|
|
@ -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
|
||||
95
BioArchLinux/shapeit4/shapeit4.patch
Normal file
95
BioArchLinux/shapeit4/shapeit4.patch
Normal file
|
|
@ -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
|
||||
Loading…
Add table
Reference in a new issue