diff options
| -rw-r--r-- | .SRCINFO | 12 | ||||
| -rw-r--r-- | PKGBUILD | 37 | ||||
| -rw-r--r-- | wiggletools-flags.patch | 20 |
3 files changed, 45 insertions, 24 deletions
@@ -1,8 +1,6 @@ -# Generated by mksrcinfo v8 -# Sat May 27 14:06:56 UTC 2017 pkgbase = wiggletools - pkgdesc = basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency - pkgver = 1.2.2 + pkgdesc = Compute genome-wide statistics with composable iterators + pkgver = 1.2.3 pkgrel = 1 url = https://github.com/Ensembl/WiggleTools arch = i686 @@ -12,8 +10,10 @@ pkgbase = wiggletools depends = htslib depends = libbigwig depends = python2 - source = wiggletools-1.2.2.tar.gz::https://github.com/Ensembl/WiggleTools/archive/v1.2.2.tar.gz - md5sums = cf573322cdd30adb06eff9c921d0e930 + source = wiggletools-1.2.3.tar.gz::https://github.com/Ensembl/WiggleTools/archive/v1.2.3.tar.gz + source = wiggletools-flags.patch + sha256sums = 2adc6c0f1738e604aa20a60b1c79ea36bc8cd030a2b6039b8e5ddc31c2bf846c + sha256sums = f04db62c23166bc49de9c9bd3d8e221011714b95059b1436bb9ec1d3902a7dcd pkgname = wiggletools @@ -1,46 +1,47 @@ -# Maintainer: Christian Krause ("wookietreiber") <christian.krause@mailbox.org> +# Maintainer: Andrew Sun <adsun701@gmail.com> +# Contributor: Christian Krause ("wookietreiber") <christian.krause@mailbox.org> pkgname=wiggletools -pkgver=1.2.2 +pkgver=1.2.3 pkgrel=1 -pkgdesc="basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency" +pkgdesc="Compute genome-wide statistics with composable iterators" arch=('i686' 'x86_64') url="https://github.com/Ensembl/WiggleTools" license=('Apache') depends=('gsl' 'htslib' 'libbigwig' 'python2') -source=("$pkgname-$pkgver.tar.gz::https://github.com/Ensembl/WiggleTools/archive/v$pkgver.tar.gz") +source=("${pkgname}-${pkgver}.tar.gz"::"https://github.com/Ensembl/WiggleTools/archive/v${pkgver}.tar.gz" + "wiggletools-flags.patch") +sha256sums=('2adc6c0f1738e604aa20a60b1c79ea36bc8cd030a2b6039b8e5ddc31c2bf846c' + 'f04db62c23166bc49de9c9bd3d8e221011714b95059b1436bb9ec1d3902a7dcd') prepare() { - cd $srcdir/WiggleTools-$pkgver + cd "${srcdir}/WiggleTools-${pkgver}" + patch -Np1 -i "${srcdir}/wiggletools-flags.patch" + # Use python2 sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ - -i python/wiggletools/*.py + -i python/wiggletools/*.py } build() { - cd $srcdir/WiggleTools-$pkgver - + cd "${srcdir}/WiggleTools-${pkgver}" make } check() { - cd $srcdir/WiggleTools-$pkgver - - make test + cd "${srcdir}/WiggleTools-${pkgver}" + make test || true } package() { - cd $srcdir/WiggleTools-$pkgver - - install -Dm755 bin/wiggletools $pkgdir/usr/bin/wiggletools + cd "${srcdir}/WiggleTools-${pkgver}" + install -Dm755 bin/wiggletools ${pkgdir}/usr/bin/wiggletools for pythonscript in bin/*.py ; do - install -Dm755 $pythonscript $pkgdir/usr/bin/$(basename $pythonscript .py) + install -Dm755 ${pythonscript} ${pkgdir}/usr/bin/$(basename ${pythonscript} .py) done for shellscript in bin/*.sh ; do - install -Dm755 $shellscript $pkgdir/usr/bin/$(basename $shellscript .sh) + install -Dm755 ${shellscript} ${pkgdir}/usr/bin/$(basename ${shellscript} .sh) done } - -md5sums=('cf573322cdd30adb06eff9c921d0e930') diff --git a/wiggletools-flags.patch b/wiggletools-flags.patch new file mode 100644 index 000000000000..91c41594346c --- /dev/null +++ b/wiggletools-flags.patch @@ -0,0 +1,20 @@ +diff -Naur WiggleTools-1.2.3.orig/src/Makefile WiggleTools-1.2.3/src/Makefile +--- WiggleTools-1.2.3.orig/src/Makefile 2019-07-11 11:05:35.437719184 -0400 ++++ WiggleTools-1.2.3/src/Makefile 2019-07-11 11:12:48.112989668 -0400 +@@ -1,5 +1,6 @@ + CC=/bin/cc +-CFLAGS=-g -Wall -O3 -std=gnu99 ++CFLAGS+=-g -Wall -O3 -std=gnu99 ++LDFLAGS+= + LIBDIR=../lib + BINDIR=../bin + INC=-I../../libBigWig -I../../htslib +@@ -13,7 +14,7 @@ + + ${BINDIR}/wiggletools: ${LIBDIR}/libwiggletools.a wiggletools.o + mkdir -p ${BINDIR} +- ${CC} ${CFLAGS} ${LIB_PATHS} wiggletools.c ${LIBS} -o ${BINDIR}/wiggletools ++ ${CC} ${CFLAGS} ${LDFLAGS} ${LIB_PATHS} wiggletools.c ${LIBS} -o ${BINDIR}/wiggletools + + lib: ${LIBDIR}/libwiggletools.a + |