Mercurial > repos > jjohnson > snpeff_with_dep
comparison tool_dependencies.xml @ 12:57c46f7fe70b
tool_dependencies.xml changes
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Sep 2012 14:42:09 -0500 |
| parents | e9e4ff80e72b |
| children | d57983929080 |
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| 11:e9e4ff80e72b | 12:57c46f7fe70b |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <set_environment version="1.0"> | 3 <set_environment version="1.0"> |
| 4 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> | 4 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/snpEff</environment_variable> |
| 5 </set_environment> | 5 </set_environment> |
| 6 <package name="snpEff" version="3.0"> | 6 <package name="snpEff" version="3.0"> |
| 7 <install version="1.0"> | 7 <install version="1.0"> |
| 8 <actions> | 8 <actions> |
| 9 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip</action> | 9 <action type="shell_command">wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff</action> |
| 10 <action type="move_file"> | 10 <action type="move_directory_files"> |
| 11 <source>snpEff_v3_0_core.zip</source> | 11 <source_directory>.</source_directory> |
| 12 <destination>$INSTALL_DIR</destination> | 12 <destination_directory>$INSTALL_DIR</destination_directory> |
| 13 </action> | 13 </action> |
| 14 <action type="shell_command">unzip snpEff_v3_0_core.zip</action> | 14 |
| 15 <action type="shell_command">ln -s snpEff_3_0 bin</action> | |
| 16 <action type="set_environment"> | 15 <action type="set_environment"> |
| 17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable> |
| 18 </action> | 17 </action> |
| 19 </actions> | 18 </actions> |
| 20 </install> | 19 </install> |
| 21 <readme> | 20 <readme> |
| 22 </readme> | 21 </readme> |