Mercurial > repos > jjohnson > krona_tools
comparison 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 |
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| 4:10132903b38b | 5:f9fc927e56c3 |
|---|---|
| 9 <destination_directory>$INSTALL_DIR</destination_directory> | 9 <destination_directory>$INSTALL_DIR</destination_directory> |
| 10 </action> | 10 </action> |
| 11 <!-- Downloaded NCBI taxonomy will be over 1.8GB after processing, Instead of $INSTALL_DIR/ maybe should be in a galaxy data dir --> | 11 <!-- Downloaded NCBI taxonomy will be over 1.8GB after processing, Instead of $INSTALL_DIR/ maybe should be in a galaxy data dir --> |
| 12 <!-- The KronaTools tar includes an empty taxonomy dir | 12 <!-- The KronaTools tar includes an empty taxonomy dir |
| 13 <action type="make_directory">$INSTALL_DIR/taxonomy</action> | 13 <action type="make_directory">$INSTALL_DIR/taxonomy</action> |
| 14 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action> | 14 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action> |
| 15 --> | 15 --> |
| 16 <!-- With prefix arg "$INSTALL_DIR" installs code into: $INSTALL_DIR/bin/ --> | 16 <!-- With prefix arg "$INSTALL_DIR" installs code into: $INSTALL_DIR/bin/ --> |
| 17 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR</action> | 17 <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR</action> |
| 18 <!-- Down load and process NCBI Taxonomy data, the updateTaxonomy.sh script relies on the curl command --> | 18 <!-- Down load and process NCBI Taxonomy data, the updateTaxonomy.sh script relies on the curl command --> |
| 19 <action type="shell_command">cd $INSTALL_DIR && if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action> | 19 <action type="shell_command">cd $INSTALL_DIR && if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action> |
| 20 <!-- copy javascript to galaxy/static/krona/ | 20 <!-- copy javascript to galaxy/static/krona/ |
| 21 <action type="shell_command">./deployResources.sh /static/krona</action> | 21 <action type="shell_command">./deployResources.sh /static/krona</action> |
| 22 --> | 22 --> |
| 23 <action type="set_environment"> | 23 <action type="set_environment"> |
| 24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |