Mercurial > repos > bebatut > humann2
changeset 5:2bf5fcf30e1f draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty
| author | bebatut |
|---|---|
| date | Fri, 18 Dec 2015 08:34:43 -0500 |
| parents | c05e34aa939b |
| children | d566de42554e |
| files | humann2.xml tool_dependencies.xml |
| diffstat | 2 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/humann2.xml Fri Dec 18 05:05:04 2015 -0500 +++ b/humann2.xml Fri Dec 18 08:34:43 2015 -0500 @@ -4,7 +4,7 @@ <requirements> <requirement type="package" version="2.2.5">bowtie2</requirement> <requirement type="package" version="2.0">metaphlan2</requirement> - <requirement type="package" version="0.6.13">diamond</requirement> + <requirement type="package" version="0.7.10">diamond</requirement> <requirement type="package" version="2.0">humann2</requirement> </requirements> @@ -47,7 +47,7 @@ --metaphlan \${METAPHLAN2_DIR}/ --metaphlan-options "-t rel_ab" --bowtie2 \${PATH} - --diamond `which diamond` + --diamond \${PATH} --threads \${GALAXY_SLOTS:-4}
--- a/tool_dependencies.xml Fri Dec 18 05:05:04 2015 -0500 +++ b/tool_dependencies.xml Fri Dec 18 08:34:43 2015 -0500 @@ -13,7 +13,8 @@ <install version="1.0"> <actions> <action type="download_by_url">https://bitbucket.org/biobakery/humann2/downloads/humann2_v0.5.0.tar.gz</action> - <action type="shell_command">python setup.py install --bypass-dependencies-install</action> + <action type="shell_command">export PYTHONPATH="$INSTALL_DIR/bin/lib/python/"</action> + <action type="shell_command">python setup.py install --home=$INSTALL_DIR/bin</action> <action type="make_directory">$INSTALL_DIR/databases</action> <action type="set_environment"> <environment_variable action="set_to" name="HUMANN2_DIR">$INSTALL_DIR/</environment_variable>