Mercurial > repos > bgruening > salmonquantmerge
diff tool-data/salmon_indexes_versioned.loc.sample @ 0:43658f594542 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
| author | bgruening |
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| date | Mon, 09 Sep 2019 11:12:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/salmon_indexes_versioned.loc.sample Mon Sep 09 11:12:04 2019 -0400 @@ -0,0 +1,32 @@ +# salmon_indexes_versioned.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Salmon. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> <version> +# +# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" + + + +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/salmon_indexes/ +# +# then the salmon_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 +# +#