Merge pull request #206 from mariux64/update-sra-tools

Update sra tools

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 </dev/null
+
+mkdir -p $PREFIX
+cat >$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