Mercurial > repos > jjohnson > krona_tools
changeset 4:10132903b38b draft
Copy files to INSTALL_DIR
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 30 Oct 2012 09:33:14 -0500 |
| parents | 3398919bc103 |
| children | f9fc927e56c3 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 10 insertions(+), 3 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Oct 29 16:05:59 2012 -0500 +++ b/tool_dependencies.xml Tue Oct 30 09:33:14 2012 -0500 @@ -4,12 +4,19 @@ <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/krona/files/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.2.tar</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> <!-- Downloaded NCBI taxonomy will be over 1.8GB after processing, Instead of $INSTALL_DIR/ maybe should be in a galaxy data dir --> + <!-- The KronaTools tar includes an empty taxonomy dir <action type="make_directory">$INSTALL_DIR/taxonomy</action> + <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action> + --> <!-- With prefix arg "$INSTALL_DIR" installs code into: $INSTALL_DIR/bin/ --> - <action type="shell_command">perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action> - <!-- Down load and process NCBI Taxonomy data --> - <action type="shell_command">./updateTaxonomy.sh</action> + <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR</action> + <!-- Down load and process NCBI Taxonomy data, the updateTaxonomy.sh script relies on the curl command --> + <action type="shell_command">cd $INSTALL_DIR && if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action> <!-- copy javascript to galaxy/static/krona/ <action type="shell_command">./deployResources.sh /static/krona</action> -->