sra-tools: Add version 3.0.0

mariux64 · Aug 15, 2022 · 9a2ae77 · 9a2ae77
1 parent ef52cb7
commit 9a2ae77
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Showing 2 changed files with 53 additions and 132 deletions.
diff --git a/sra-tools-2.11.2.build.sh b/sra-tools-2.11.2.build.sh
diff --git a/sra-tools-2.11.2-0.build.sh → sra-tools-3.0.0-0.build.sh b/sra-tools-2.11.2-0.build.sh → sra-tools-3.0.0-0.build.sh
@@ -1,7 +1,9 @@
-#! /bin/bash
+#! /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=2.11.2
+VERSION=3.0.0
 BUILD=0
 
 PREFIX=/pkg/$PKG-$VERSION-$BUILD
@@ -10,9 +12,9 @@ if [ -n "$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/${VERSION}.tar.gz"
+#NGS="https://github.com/ncbi/ngs-tools/archive/refs/tags/${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`
@@ -38,7 +40,7 @@ function get_extract () {
 set -xe
 umask 022
 
-BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
+BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.build.tmp
 test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR
 mkdir -p $BUILD_TMPDIR/home
 export TMPDIR=$BUILD_TMPDIR
@@ -54,15 +56,21 @@ cat >$PREFIX/profile <<-EOF
 EOF
 . $PREFIX/profile
 
-export MAKEFLAGS="-j $(nproc)"
+NJOBS=$(( $(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
 
@@ -72,37 +80,58 @@ do
 	get_extract $i
 done
 
+ngstools-build() {
+
 cd ${BUILDDIR}/${NGS_DIR}
 
-./configure --prefix=${PREFIX} \
-            --build-prefix=${BUILDDIR}/ngs-outdir
+echo -e "\n\n++++++++++++++ngs+++++++++++++++++\n\n"
+
+}
 
-make -C ngs-sdk
-make -C ngs-java
+#ngs-build()
 
-make -C ngs-sdk install
-make -C ngs-java install
+vdb-build() {
 
 cd ${BUILDDIR}/${VDB_DIR}
 
-./configure --prefix=${PREFIX} \
-            --with-ngs-sdk-prefix=${BUILDDIR}/ngs-outdir \
-            --build-prefix=${BUILDDIR}/ncbi-outdir
-
-make
+cmake -DCMAKE_INSTALL_PREFIX=${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}
 
-./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
+test -d obj || mkdir obj
+cd obj
+test -e ngs || ln -s ../ngs .
 
-VDB_SRCDIR=${BUILDDIR}/${VDB_DIR} make
+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