diff --git a/sra-tools-3.0.0-0.build.sh b/sra-tools-3.0.0-0.build.sh new file mode 100755 index 0000000..e041a49 --- /dev/null +++ b/sra-tools-3.0.0-0.build.sh @@ -0,0 +1,137 @@ +#! /bin/bash -x + +COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.2; exec bash /dev/shm/runme-$COOKIE.sh $1 + +PKG=sra-tools +VERSION=3.0.0 +BUILD=0 + +PREFIX=/pkg/$PKG-$VERSION-$BUILD +if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi + +ARCHIVE=${PREFIX}/build/archive + +#URL's +#NGS="https://github.com/ncbi/ngs-tools/archive/refs/tags/${VERSION}.tar.gz" +VDB="https://github.com/ncbi/ncbi-vdb/archive/refs/tags/${VERSION}.tar.gz" +SRA="https://github.com/ncbi/sra-tools/archive/refs/tags/${VERSION}.tar.gz" + +#BUILD Dirs +NGS_DIR=`echo $NGS |cut -d"/" -f5` +VDB_DIR=`echo $VDB |cut -d"/" -f5` +SRA_DIR=`echo $SRA |cut -d"/" -f5` + +function get_extract () { + pkg=`echo ${1} |cut -d"/" -f7` + dir=`echo ${1} |cut -d"/" -f5` + arc=${ARCHIVE}/${dir}-${pkg} + if [ ! -e ${arc} ] + then + wget ${1} -O ${arc} + fi + if [ ! -e $dir ] + then + mkdir $dir + tar -xof ${arc} -C ${dir} --strip-components 1 --checkpoint=1000 + fi +} + + +set -xe +umask 022 + +BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH + LD_LIBRARY_PATH=$PREFIX/lib:\$LD_LIBRARY_PATH + export PATH LD_LIBRARY_PATH +EOF +. $PREFIX/profile + +NJOBS=$(( $(nproc) * 4 / 5 + 1 )) + +export MAKEFLAGS="-j $NJOBS" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR + +cd $PREFIX +if [ ! -e lib ]; then +mkdir lib +fi +if [ ! -e lib64 ]; then +ln -s lib lib64 +fi + +cd $BUILDDIR + +test -d ${ARCHIVE} || mkdir ${ARCHIVE} +for i in $NGS $VDB $SRA; +do + get_extract $i +done + +ngstools-build() { + +cd ${BUILDDIR}/${NGS_DIR} + +echo -e "\n\n++++++++++++++ngs+++++++++++++++++\n\n" + +} + +#ngs-build() + +vdb-build() { + +cd ${BUILDDIR}/${VDB_DIR} + +cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} \ +. +make ${MAKEFLAGS} + +make install + +} + +vdb-build + +#ngs-build() { + #jetzt neu im repo von sratools +#} + +sratools-build() { + +echo -e "\n\n++++++++++++++sra-tools++++++++++++++++\n\n" + +cd ${BUILDDIR}/${SRA_DIR} + +test -d obj || mkdir obj +cd obj +test -e ngs || ln -s ../ngs . + +cd ${BUILDDIR}/${SRA_DIR} + +cmake \ + -DCMAKE_INSTALL_PREFIX=${PREFIX} \ + -DVDB_LIBDIR=${PREFIX}/lib \ + -DVDB_BINDIR=${BUILDDIR}/${VDB_DIR} \ + -DVDB_INCDIR=${BUILDDIR}/${VDB_DIR}/interfaces \ + -DCMAKE_VERBOSE_MAKEFILE=ON \ + . + +make ${MAKEFLAGS} + +make install +} +sratools-build + +exit