Mercurial > repos > jjohnson > snpeff_with_dep
annotate tool_dependencies.xml @ 7:3cb1d19d57d1
Remove download at end of url
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 14 Sep 2012 14:07:09 -0500 |
| parents | e6b662b96061 |
| children | 1562bb333568 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <set_environment version="1.0"> | |
| 4 | 4 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> |
| 0 | 5 </set_environment> |
| 6 <package name="snpEff" version="3.0f"> | |
| 7 <install version="1.0"> | |
| 8 <actions> | |
| 7 | 9 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip</action> |
|
2
5248f48fa4ee
Add debug actions to tool_dependencies
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
10 <action type="shell_command">pwd</action> |
|
5248f48fa4ee
Add debug actions to tool_dependencies
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
11 <action type="shell_command">ls</action> |
| 4 | 12 <action type="move_file"> |
| 13 <source>SnpSift.jar</source> | |
| 14 <destination>$INSTALL_DIR/bin</destination> | |
| 15 </action> | |
| 16 <action type="move_file"> | |
| 17 <source>snpEff.jar</source> | |
| 18 <destination>$INSTALL_DIR/bin</destination> | |
| 19 </action> | |
| 20 <action type="move_directory_files"> | |
| 21 <source_directory>scripts</source_directory> | |
| 22 <destination_directory>$INSTALL_DIR/bin</destination_directory> | |
| 23 </action> | |
| 24 <action type="move_file"> | |
| 25 <source>snpEff.config</source> | |
| 26 <destination>$INSTALL_DIR/bin</destination> | |
| 27 </action> | |
| 28 <action type="set_environment"> | |
| 6 | 29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
| 4 | 30 </action> |
| 0 | 31 </actions> |
| 32 </install> | |
| 33 <readme> | |
| 34 </readme> | |
| 35 </package> | |
| 36 | |
| 37 </tool_dependency> | |
| 38 |