Mercurial > repos > bebatut > metaphlan2
changeset 33:e8206e14e889 draft
Uploaded
| author | bebatut |
|---|---|
| date | Wed, 22 Feb 2017 09:16:03 -0500 |
| parents | c941148c75c7 |
| children | 476d18d599c9 |
| files | metaphlan2.xml repository_dependencies.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/metaphlan2.xml Wed Feb 22 03:49:35 2017 -0500 +++ b/metaphlan2.xml Wed Feb 22 09:16:03 2017 -0500 @@ -45,9 +45,9 @@ #if $db.db_selector == "cached" #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data]) #set $db_choice = $db.cached_db.value - #set $metadata = `ls $paths[$db_choice]/*.pkl` - --bowtie2db $metadata[:-4] - --mpa_pkl '$metadata' + metadata=`ls $paths[$db_choice]/*.pkl` + --bowtie2db `echo $metadata | sed 's/\(.*\)\..*/\1/'` + --mpa_pkl \$metadata #else --bowtie2db 'ref_db/ref_db' --mpa_pkl 'ref_db/metadata.pkl'
--- a/repository_dependencies.xml Wed Feb 22 03:49:35 2017 -0500 +++ b/repository_dependencies.xml Wed Feb 22 09:16:03 2017 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases."> - <repository changeset_revision="332cb1b3b349" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="dbfade666d42" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>