Mercurial > repos > matt-shirley > ncbi_sra_toolkit
comparison tool_dependencies.xml @ 16:dd337a830b5c
Use patched versions of tools.
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 16:22:27 -0400 |
| parents | c71031b17e08 |
| children | a8261e9cbe13 |
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| 15:c71031b17e08 | 16:dd337a830b5c |
|---|---|
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions> |
| 6 <action type="make_directory">src</action> | 6 <action type="make_directory">src</action> |
| 7 <action type="make_directory">build</action> | 7 <action type="make_directory">build</action> |
| 8 <action type="change_directory">src</action> | 8 <action type="change_directory">src</action> |
| 9 <action type="shell_command">git clone https://github.com/ncbi/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/ncbi/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/ncbi/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">ncbi-vdb</action> | 13 <action type="change_directory">ncbi-vdb</action> |
| 14 <action type="shell_command">git checkout bf5ffdd</action> | |
| 15 <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> |
| 16 <action type="change_directory">../ngs</action> | 15 <action type="change_directory">../ngs</action> |
| 17 <action type="shell_command">git checkout 3a7a0ed</action> | |
| 18 <action type="change_directory">ngs-sdk</action> | 16 <action type="change_directory">ngs-sdk</action> |
| 19 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> | 17 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> |
| 20 <action type="change_directory">../../sra-tools</action> | 18 <action type="change_directory">../../sra-tools</action> |
| 21 <action type="shell_command">git checkout 4ef7ea0</action> | |
| 22 <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=$INSTALL_DIR --with-magic-prefix=/dev/null</action> | 19 <action type="autoconf">--prefix=$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> |
| 23 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> | 20 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> |
| 24 </actions> | 21 </actions> |
| 25 </install> | 22 </install> |
| 26 <readme> | 23 <readme> |