Merge pull request #141 from mariux64/sra-tools-update

Sra tools update

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 </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
+
+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