Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison tool_dependencies.xml @ 18:3da3d1a4deae

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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
comparison
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17:a8261e9cbe13 18:3da3d1a4deae
8 <action type="change_directory">src</action> 8 <action type="change_directory">src</action>
9 <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action> 9 <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action>
10 <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action> 10 <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action>
11 <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action> 11 <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action>
12 <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action> 12 <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action>
13 <action type="change_directory">$INSTALL_DIR/src/ncbi-vdb</action> 13 <action type="shell_command">cd $INSTALL_DIR/src/ncbi-vdb</action>
14 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> 14 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
15 <action type="change_directory">$INSTALL_DIR/src/ngs/ngs-sdk</action> 15 <action type="shell_command">cd $INSTALL_DIR/src/ngs/ngs-sdk</action>
16 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> 16 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
17 <action type="change_directory">$INSTALL_DIR/src/sra-tools</action> 17 <action type="shell_command"> cd $INSTALL_DIR/src/sra-tools</action>
18 <action type="autoconf">--prefix=$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> 18 <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=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
19 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> 19 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
20 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> 20 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
21 </actions> 21 </actions>
22 </install> 22 </install>