Mercurial > repos > matt-shirley > ncbi_sra_toolkit
diff tool_dependencies.xml @ 18:3da3d1a4deae
Back to shell commands. Maybe change_directory directive does not support reading env variables?
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 20:31:50 -0400 |
| parents | a8261e9cbe13 |
| children | 6d25dfb4dbb4 |
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--- 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 @@ <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action> <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action> <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action> - <action type="change_directory">$INSTALL_DIR/src/ncbi-vdb</action> + <action type="shell_command">cd $INSTALL_DIR/src/ncbi-vdb</action> <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> - <action type="change_directory">$INSTALL_DIR/src/ngs/ngs-sdk</action> + <action type="shell_command">cd $INSTALL_DIR/src/ngs/ngs-sdk</action> <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> - <action type="change_directory">$INSTALL_DIR/src/sra-tools</action> + <action type="shell_command"> cd $INSTALL_DIR/src/sra-tools</action> <action type="autoconf">--prefix=$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</action> <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>