Mercurial > repos > jjohnson > metaphlan
changeset 3:51288d868a5c draft
tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 10 Oct 2012 08:33:33 -0500 |
| parents | d90db1d506c4 |
| children | 3468e70d3ed0 |
| files | metaphlan.xml tool_dependencies.xml |
| diffstat | 2 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/metaphlan.xml Tue Oct 09 20:54:18 2012 -0500 +++ b/metaphlan.xml Wed Oct 10 08:33:33 2012 -0500 @@ -1,6 +1,5 @@ <tool id="metaphlan" name="MetaPhlAn" version="1.7.0"> <requirements> - <requirement type="set_environment">METAPHLAN_BASE</requirement> <requirement type="package" version="1.7.0">metaphlan</requirement> <requirement type="package">bowtie2</requirement> </requirements> @@ -8,7 +7,7 @@ <command> metaphlan.py $input - --bowtie2db ${METAPHLAN_BASE}/bowtie2db/mpa + --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa --no_map -o $output --bt2_ps $PresetsForBowtie2
--- a/tool_dependencies.xml Tue Oct 09 20:54:18 2012 -0500 +++ b/tool_dependencies.xml Wed Oct 10 08:33:33 2012 -0500 @@ -1,15 +1,20 @@ <?xml version="1.0"?> <tool_dependency> - <set_environment version="1.0"> - <environment_variable name="METAPHLAN_BASE" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> <package name="metaphlan" version="1.7.0"> <install version="1.0"> <actions> <action type="shell_command">hg clone http://bitbucket.org/nsegata/metaphlan</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> + <action type="set_environment"> + <environment_variable name="METAPHLAN_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> </install> <readme>