diff options
| -rw-r--r-- | .SRCINFO | 17 | ||||
| -rw-r--r-- | .gitignore | 5 | ||||
| -rw-r--r-- | PKGBUILD | 45 |
3 files changed, 67 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..9a417df41fea --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,17 @@ +pkgbase = cufflinks-git + pkgdesc = Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.. + pkgver = v2.2.1.r83.gb4fa050 + pkgrel = 1 + url = http://cole-trapnell-lab.github.io/projects/cufflinks/ + arch = x86_64 + license = Artistic + depends = boost + depends = eigen3 + depends = python2 + depends = samtools + depends = perl + source = git+https://github.com/cole-trapnell-lab/cufflinks.git + md5sums = SKIP + +pkgname = cufflinks-git + diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000000..e4a758110fea --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +/src +/pkg +*.tar.gz +*.tar.xz +*.pkg.tar diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..53a4c8af1748 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,45 @@ +# Maintainer: Grey Christoforo <first name @ last name .net> + +pkgname=cufflinks-git +pkgver=v2.2.1.r83.gb4fa050 +pkgrel=1 +pkgdesc="Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.." +arch=("x86_64") +url="http://cole-trapnell-lab.github.io/projects/cufflinks/" +license=('Artistic') +depends=('boost' 'eigen3' 'python2' 'samtools' 'perl') +source=('git+https://github.com/cole-trapnell-lab/cufflinks.git') +md5sums=('SKIP') + +pkgver() { + cd cufflinks + git describe --long | sed 's/\([^-]*-g\)/r\1/;s/-/./g' +} + +prepare() { + cd cufflinks + + sed -i 's,hash\[pos\]\.hash,(hash[pos].hash),g' src/GHash.hh + + + + ./autogen.sh + # cufflinks uses python2 but archlinux uses python3 as default python + perl -i -pne '$_ =~ s/python/python2/ if $_ =~ /^#!\/usr/' src/cuffmerge + + export EIGEN_CPPFLAGS="-I/usr/include/eigen3" + export LDFLAGS="-L/usr/lib -lboost_system" + ./configure --prefix=/usr +} + +build() { + cd cufflinks + export EIGEN_CPPFLAGS="-I/usr/include/eigen3" + export LDFLAGS="-L/usr/lib -lboost_system" + make +} + +package(){ + cd cufflinks + make DESTDIR="$pkgdir/" install +} |