Mercurial > repos > jjohnson > krona_tools
annotate tool_dependencies.xml @ 5:f9fc927e56c3 draft
xml escapes in tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 30 Oct 2012 12:25:52 -0500 |
| parents | 10132903b38b |
| children | c74f1ea02e29 |
| rev | line source |
|---|---|
| 1 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="KronaTools" version="2.2"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://sourceforge.net/projects/krona/files/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.2.tar</action> | |
| 4 | 7 <action type="move_directory_files"> |
| 8 <source_directory>.</source_directory> | |
| 9 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 10 </action> | |
| 3 | 11 <!-- Downloaded NCBI taxonomy will be over 1.8GB after processing, Instead of $INSTALL_DIR/ maybe should be in a galaxy data dir --> |
| 4 | 12 <!-- The KronaTools tar includes an empty taxonomy dir |
| 1 | 13 <action type="make_directory">$INSTALL_DIR/taxonomy</action> |
|
5
f9fc927e56c3
xml escapes in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
14 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action> |
| 4 | 15 --> |
| 3 | 16 <!-- With prefix arg "$INSTALL_DIR" installs code into: $INSTALL_DIR/bin/ --> |
|
5
f9fc927e56c3
xml escapes in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
17 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR</action> |
| 4 | 18 <!-- Down load and process NCBI Taxonomy data, the updateTaxonomy.sh script relies on the curl command --> |
|
5
f9fc927e56c3
xml escapes in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
19 <action type="shell_command">cd $INSTALL_DIR && if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action> |
| 3 | 20 <!-- copy javascript to galaxy/static/krona/ |
| 1 | 21 <action type="shell_command">./deployResources.sh /static/krona</action> |
| 22 --> | |
| 23 <action type="set_environment"> | |
| 24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 25 </action> | |
| 26 </actions> | |
| 27 </install> | |
| 28 <readme>http://sourceforge.net/p/krona/home/krona/</readme> | |
| 29 </package> | |
| 30 </tool_dependency> |