Mercurial > repos > george-weingart > metaphlan2_hutlab
changeset 10:4f3ae60396f9 draft
Uploaded
| author | george-weingart |
|---|---|
| date | Mon, 25 Apr 2016 00:32:57 -0400 |
| parents | 16fd605f31de |
| children | 0e82a9af69ab |
| files | metaphlan2_hutlab/metaphlan2.xml metaphlan2_hutlab/tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 14 deletions(-) [+] |
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--- a/metaphlan2_hutlab/metaphlan2.xml Mon Apr 25 00:09:30 2016 -0400 +++ b/metaphlan2_hutlab/metaphlan2.xml Mon Apr 25 00:32:57 2016 -0400 @@ -5,8 +5,8 @@ <description>metagenomic profiler V2</description> <command interpreter="python">metaphlan2.py $input - --mpa_pkl \${METAPHLAN2_PATH}/db_v20/mpa_v20_m200.pkl - --bowtie2db \${METAPHLAN2_PATH}/db_v20/mpa_v20_m200 + --mpa_pkl $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200.pkl + --bowtie2db $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200 --input_type fastq --no_map --bt2_ps $PresetsForBowtie2
--- a/metaphlan2_hutlab/tool_dependencies.xml Mon Apr 25 00:09:30 2016 -0400 +++ b/metaphlan2_hutlab/tool_dependencies.xml Mon Apr 25 00:32:57 2016 -0400 @@ -1,15 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <install version="1.0"> - <actions> - <action type="shell_command">hg clone https://bitbucket.org/biobakery/metaphlan2 metaphlan2_hutlab</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="METAPHLAN2_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - - </actions> - </install> + <set_environment version="1.0"> + <environment_variable name="METAPHLAN2_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> </tool_dependency>