diff --git a/sra-tools-2.10.8-0.build.sh b/sra-tools-2.10.8-0.build.sh new file mode 100755 index 0000000..0fffd20 --- /dev/null +++ b/sra-tools-2.10.8-0.build.sh @@ -0,0 +1,108 @@ +#! /bin/bash + +PKG=sra-tools +VERSION=2.10.8 +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/archive/${VERSION}.tar.gz" +VDB="https://github.com/ncbi/ncbi-vdb/archive/${VERSION}.tar.gz" +SRA="https://github.com/ncbi/sra-tools/archive/${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 ${dir} --strip-components 1 --checkpoint=1000 + fi +} + + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$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 + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR + +cd $PREFIX +mkdir lib +ln -s lib lib64 + +cd $BUILDDIR + +test -d ${ARCHIVE} || mkdir ${ARCHIVE} +for i in $NGS $VDB $SRA; +do + get_extract $i +done + +cd ${BUILDDIR}/${NGS_DIR} + +./configure --prefix=${PREFIX} \ + --build-prefix=${BUILDDIR}/ngs-outdir + +make -C ngs-sdk +make -C ngs-java + +make -C ngs-sdk install +make -C ngs-java install + +cd ${BUILDDIR}/${VDB_DIR} + +./configure --prefix=${PREFIX} \ + --with-ngs-sdk-prefix=${BUILDDIR}/ngs-outdir \ + --build-prefix=${BUILDDIR}/ncbi-outdir + +make + +make install + +cd ${BUILDDIR}/${SRA_DIR} + +./configure --with-ngs-sdk-prefix=${BUILDDIR}/ngs-outdir \ + --with-ncbi-vdb-sources=${BUILDDIR}/${VDB_DIR} \ + --with-ncbi-vdb-build=${BUILDDIR}/ncbi-outdir \ + --prefix=${PREFIX} \ + --build-prefix=${BUILDDIR}/sra-tools-outdir + +VDB_SRCDIR=${BUILDDIR}/${VDB_DIR} make + +make install + +exit