v2.19.0 - initial commit

1 files changed, 53 insertions, 0 deletions

diff --git a/PKGBUILD b/PKGBUILD
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+# 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
+
+
+}