Mercurial > repos > jjohnson > metaphlan
changeset 1:868624c77941 draft
Add tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 09 Oct 2012 15:53:06 -0500 |
| parents | 0ec6c5781381 |
| children | d90db1d506c4 |
| files | metaphlan.xml tool_dependencies.xml |
| diffstat | 2 files changed, 27 insertions(+), 4 deletions(-) [+] |
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--- a/metaphlan.xml Tue Oct 09 12:13:27 2012 -0400 +++ b/metaphlan.xml Tue Oct 09 15:53:06 2012 -0500 @@ -1,13 +1,14 @@ -<tool id="metaphlan" name="MetaPhlAn" version="1.6.0"> +<tool id="metaphlan" name="MetaPhlAn" version="1.7.0"> <requirements> -<requirement type="package">metaphlan</requirement> -<requirement type="package">bowtie2</requirement> + <requirement type="set_environment">METAPHLAN_BASE</requirement> + <requirement type="package" version="1.7.0">metaphlan</requirement> + <requirement type="package">bowtie2</requirement> </requirements> <description>Metagenomic Phylogenetic Analysis</description> <command> metaphlan.py $input - --bowtie2db ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan/bowtie2db/mpa + --bowtie2db ${METAPHLAN_BASE}/bowtie2db/mpa --no_map -o $output --bt2_ps $PresetsForBowtie2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 09 15:53:06 2012 -0500 @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="METAPHLAN_BASE" action="set_to">$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 https://bitbucket.org/nsegata/metaphlan -u 43684e5f6dc5</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for the metaphlan package: +http://huttenhower.sph.harvard.edu/metaphlan +https://groups.google.com/forum/#!forum/metaphlan-users + </readme> + </package> +</tool_dependency> +