Mercurial > repos > matt-shirley > ncbi_sra_toolkit
comparison tool_dependencies.xml @ 12:d45b5bdcff3f
Don't use builtin change_directory directive
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 14:27:49 -0400 |
| parents | 91558de676f4 |
| children | 3369a52a5934 |
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| 11:91558de676f4 | 12:d45b5bdcff3f |
|---|---|
| 13 <action type="make_directory">$NCBI</action> | 13 <action type="make_directory">$NCBI</action> |
| 14 <action type="change_directory">$NCBI</action> | 14 <action type="change_directory">$NCBI</action> |
| 15 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action> | 15 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action> |
| 16 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action> | 16 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action> |
| 17 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action> | 17 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action> |
| 18 <action type="change_directory">$NCBI/ncbi-vdb</action> | 18 <action type="shell_command">cd $NCBI/ncbi-vdb</action> |
| 19 <action type="shell_command">git checkout bf5ffdd</action> | 19 <action type="shell_command">git checkout bf5ffdd</action> |
| 20 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> | 20 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> |
| 21 <action type="change_directory">$NCBI/ngs</action> | 21 <action type="shell_command">cd $NCBI/ngs</action> |
| 22 <action type="shell_command">git checkout 3a7a0ed</action> | 22 <action type="shell_command">git checkout 3a7a0ed</action> |
| 23 <action type="change_directory">$NCBI/ngs/ngs-sdk</action> | 23 <action type="shell_command">cd $NCBI/ngs/ngs-sdk</action> |
| 24 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> | 24 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> |
| 25 <action type="change_directory">$NCBI/sra-tools</action> | 25 <action type="shell_command">cd $NCBI/sra-tools</action> |
| 26 <action type="shell_command">git checkout 4ef7ea0</action> | 26 <action type="shell_command">git checkout 4ef7ea0</action> |
| 27 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD --with-ncbi-vdb-build=$BUILD --with-ncbi-vdb-sources=$NCBI/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action> | 27 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD --with-ncbi-vdb-build=$BUILD --with-ncbi-vdb-sources=$NCBI/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action> |
| 28 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> | 28 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> |
| 29 </actions> | 29 </actions> |
| 30 </install> | 30 </install> |