# HG changeset patch # User Matt Shirley # Date 1427761910 14400 # Node ID 3da3d1a4deaef2375e5b3fe042ca23ba355c6381 # Parent a8261e9cbe137b7479ad82ee52fa7deae228fe10 Back to shell commands. Maybe change_directory directive does not support reading env variables? diff -r a8261e9cbe13 -r 3da3d1a4deae tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 30 20:24:04 2015 -0400 +++ b/tool_dependencies.xml Mon Mar 30 20:31:50 2015 -0400 @@ -10,11 +10,11 @@ git clone https://github.com/mdshw5/ncbi-vdb.git git clone https://github.com/mdshw5/ngs.git LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib - $INSTALL_DIR/src/ncbi-vdb + cd $INSTALL_DIR/src/ncbi-vdb --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build - $INSTALL_DIR/src/ngs/ngs-sdk + cd $INSTALL_DIR/src/ngs/ngs-sdk --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build - $INSTALL_DIR/src/sra-tools + cd $INSTALL_DIR/src/sra-tools --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg $INSTALL_DIR/bin