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Merge pull request #44 from ICGC-TCGA-PanCancer/dev
v1.1.1
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Original file line number | Diff line number | Diff line change |
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@@ -36,4 +36,5 @@ requires: | |
Term::UI: 0.42 | ||
Test::Fatal: 0.013 | ||
Try::Tiny: 0.19 | ||
version: v1.1.0 | ||
XML::Simple: 2.2 | ||
version: v1.1.1 |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,124 @@ | ||
#! /bin/bash | ||
LIBMAUSVERSION=0.0.130-release-20140618101704 | ||
BIOBAMBAMVERSION=0.0.148-release-20140618101902 | ||
SNAPPYVERSION=1.1.1 | ||
IOLIBVERSION=1.13.7 | ||
CHRPATHVERSION=0.16 | ||
BUILDDIR=${PWD} | ||
INSTALLDIR=${BUILDDIR}/install-dir | ||
TOOLSDIR=${BUILDDIR}/tools-dir | ||
PAR=`cat /proc/cpuinfo | egrep "^processor" | wc -l` | ||
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# get chrpath | ||
if [ ! -f chrpath-${CHRPATHVERSION}.tar.gz ] ; then | ||
wget -O - "https://alioth.debian.org/frs/download.php/file/3979/chrpath-${CHRPATHVERSION}.tar.gz" > chrpath-${CHRPATHVERSION}.tar.gz | ||
fi | ||
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# get iolib | ||
if [ ! -f io_lib-${IOLIBVERSION}.tar.gz ] ; then | ||
wget -O - "http://downloads.sourceforge.net/project/staden/io_lib/${IOLIBVERSION}/io_lib-${IOLIBVERSION}.tar.gz?&use_mirror=kent" \ | ||
> io_lib-${IOLIBVERSION}.tar.gz | ||
fi | ||
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||
# get snappy | ||
if [ ! -f snappy-${SNAPPYVERSION}.tar.gz ] ; then | ||
wget -O - https://snappy.googlecode.com/files/snappy-${SNAPPYVERSION}.tar.gz > snappy-${SNAPPYVERSION}.tar.gz | ||
fi | ||
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# get libmaus | ||
if [ ! -f libmaus-${LIBMAUSVERSION}.tar.gz ] ; then | ||
wget -O - https://github.com/gt1/libmaus/archive/${LIBMAUSVERSION}.tar.gz > libmaus-${LIBMAUSVERSION}.tar.gz | ||
fi | ||
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# get biobambam | ||
if [ ! -f biobambam-${BIOBAMBAMVERSION}.tar.gz ] ; then | ||
wget -O - https://github.com/gt1/biobambam/archive/${BIOBAMBAMVERSION}.tar.gz > biobambam-${BIOBAMBAMVERSION}.tar.gz | ||
fi | ||
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tar xzvf chrpath-${CHRPATHVERSION}.tar.gz | ||
mv chrpath-${CHRPATHVERSION} chrpath-${CHRPATHVERSION}-src | ||
mkdir -p chrpath-${CHRPATHVERSION}-build | ||
cd chrpath-${CHRPATHVERSION}-build | ||
${BUILDDIR}/chrpath-${CHRPATHVERSION}-src/configure --prefix=${TOOLSDIR} | ||
make -j${PAR} | ||
make -j${PAR} install | ||
cd .. | ||
rm -fR chrpath-${CHRPATHVERSION}-src chrpath-${CHRPATHVERSION}-build | ||
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rm -fR ${INSTALLDIR} | ||
mkdir -p ${INSTALLDIR} | ||
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# build iolib | ||
tar xzvf io_lib-${IOLIBVERSION}.tar.gz | ||
mv io_lib-${IOLIBVERSION} io_lib-${IOLIBVERSION}-src | ||
mkdir -p io_lib-${IOLIBVERSION}-build | ||
cd io_lib-${IOLIBVERSION}-build | ||
LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/io_lib-${IOLIBVERSION}-src/configure --prefix=${INSTALLDIR} | ||
make -j${PAR} | ||
make -j${PAR} install | ||
cd .. | ||
rm -fR io_lib-${IOLIBVERSION}-src io_lib-${IOLIBVERSION}-build | ||
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# build snappy | ||
tar xzvf snappy-${SNAPPYVERSION}.tar.gz | ||
mv snappy-${SNAPPYVERSION} snappy-${SNAPPYVERSION}-src | ||
mkdir -p snappy-${SNAPPYVERSION}-build | ||
cd snappy-${SNAPPYVERSION}-build | ||
LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/snappy-${SNAPPYVERSION}-src/configure --prefix=${INSTALLDIR} | ||
make -j${PAR} | ||
make -j${PAR} install | ||
cd .. | ||
rm -fR snappy-${SNAPPYVERSION}-src snappy-${SNAPPYVERSION}-build | ||
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# build libmaus | ||
tar xzvf libmaus-${LIBMAUSVERSION}.tar.gz | ||
mv libmaus-${LIBMAUSVERSION} libmaus-${LIBMAUSVERSION}-src | ||
mkdir -p libmaus-${LIBMAUSVERSION}-build | ||
cd libmaus-${LIBMAUSVERSION}-build | ||
LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/libmaus-${LIBMAUSVERSION}-src/configure --prefix=${INSTALLDIR} \ | ||
--with-snappy=${INSTALLDIR} \ | ||
--with-io_lib=${INSTALLDIR} | ||
make -j${PAR} | ||
make -j${PAR} install | ||
cd .. | ||
rm -fR libmaus-${LIBMAUSVERSION}-src libmaus-${LIBMAUSVERSION}-build | ||
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# build biobambam | ||
tar xzvf biobambam-${BIOBAMBAMVERSION}.tar.gz | ||
mv biobambam-${BIOBAMBAMVERSION} biobambam-${BIOBAMBAMVERSION}-src | ||
mkdir -p biobambam-${BIOBAMBAMVERSION}-build | ||
cd biobambam-${BIOBAMBAMVERSION}-build | ||
LDFLAGS="-Wl,-rpath=XORIGIN/../lib" ${BUILDDIR}/biobambam-${BIOBAMBAMVERSION}-src/configure --prefix=${INSTALLDIR} \ | ||
--with-libmaus=${INSTALLDIR} | ||
make -j${PAR} | ||
make -j${PAR} install | ||
cd .. | ||
rm -fR biobambam-${BIOBAMBAMVERSION}-src biobambam-${BIOBAMBAMVERSION}-build | ||
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for i in `find ${INSTALLDIR} -name \*.so\*` ; do | ||
ORIG=`objdump -x ${i} | grep RPATH | awk '{print $2}'` | ||
MOD=`echo "$ORIG" | sed "s/XORIGIN/\\$ORIGIN/"` | ||
${TOOLSDIR}/bin/chrpath -r "${MOD}" ${i} | ||
done | ||
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for i in ${INSTALLDIR}/bin/* ; do | ||
if [ ! -z `LANG=C file ${i} | egrep "ELF.*executable" | awk '{print $1}' | perl -p -e "s/://"` ] ; then | ||
ORIG=`objdump -x ${i} | grep RPATH | awk '{print $2}'` | ||
MOD=`echo "$ORIG" | sed "s/XORIGIN/\\$ORIGIN/"` | ||
${TOOLSDIR}/bin/chrpath -r "${MOD}" ${i} | ||
fi | ||
done | ||
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#mv ${INSTALLDIR} biobambam-${BIOBAMBAMVERSION} | ||
#tar czvf biobambam-${BIOBAMBAMVERSION}-`uname -p`-`uname -s`.tar.gz biobambam-${BIOBAMBAMVERSION} | ||
#rm -fR biobambam-${BIOBAMBAMVERSION} | ||
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rm -fR ${TOOLSDIR} | ||
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# my additions | ||
mv ${INSTALLDIR} biobambam | ||
rm -f chrpath-${CHRPATHVERSION}.tar.gz | ||
rm -f io_lib-${IOLIBVERSION}.tar.gz | ||
rm -f snappy-${SNAPPYVERSION}.tar.gz | ||
rm -f libmaus-${LIBMAUSVERSION}.tar.gz | ||
rm -f biobambam-${BIOBAMBAMVERSION}.tar.gz |
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