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| -rw-r--r-- | .SRCINFO | 16 | ||||
| -rw-r--r-- | PKGBUILD | 53 |
2 files changed, 69 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..2babffa58eec --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,16 @@ +pkgbase = bcl2fastq + pkgdesc = Demultiplexes data and converts BCL files generated by Illumina sequencers to FASTQ for downstream analysis. + pkgver = 2.19.0 + pkgrel = 1 + url = https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html + arch = i686 + arch = x86_64 + license = custom + options = !emptydirs + source = https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2.19.0.tar.gz + source = http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz + md5sums = 1778aa271d7af8cbf9d1065994603a30 + md5sums = 93780777cfbf999a600f62883bd54b17 + +pkgname = bcl2fastq + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..c4c966414e72 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: Fabio Zanini <fabio _DOT zanini AT_ fastmail DOT_ fm> +pkgname=bcl2fastq +pkgver=2.19.0 +pkgrel=1 +pkgdesc='Demultiplexes data and converts BCL files generated by Illumina sequencers to FASTQ for downstream analysis.' +arch=('i686' 'x86_64') +url="https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html" +license=('custom') +#depends=('python-matplotlib') +makedeps=('gcc>=4.9') +source=("https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v${pkgver}.tar.gz" "http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz") +md5sums=('1778aa271d7af8cbf9d1065994603a30' '93780777cfbf999a600f62883bd54b17') +options=('!emptydirs') + +build() { + # get boost 1.55, correct its python invocation, and fake it as 1.54 for bcl2fastq + msg "Fix python2 in boost bootstrap" + sed -i 's/PYTHON=python/PYTHON=python2.7/' "${srcdir}/boost_1_55_0/bootstrap.sh" + + msg "Fake boost 1.54 with boost 1.55" + cd "${srcdir}" + rm -rf boost_1_54_0 + mv boost_1_55_0 boost_1_54_0 + tar -cf boost_1_54_0.tar boost_1_54_0 && bzip2 boost_1_54_0.tar + rm bcl2fastq/redist/boost_1_54_0.tar.bz2 + cp boost_1_54_0.tar.bz2 bcl2fastq/redist/ + + msg "Make build folder" + cd "${srcdir}" + rm -rf "${srcdir}/build" + mkdir -p "${srcdir}/build" + cd build + + msg "Configure bcl2fastq" + "${srcdir}/${pkgname}/src/configure" --prefix="${pkgdir}" + + msg "Make bcl2fastq" + make -j2 +} + +package() { + cd "${srcdir}/build" + make install + + # illumina uses folders + install -d "${pkgdir}"/usr/bin + mv "${pkgdir}"/bin/bcl2fastq "${pkgdir}"/usr/bin/bcl2fastq + rm -rf "${pkgdir}"/bin + + mv "${pkgdir}"/share "${pkgdir}"/usr/share + + +} |