Mercurial > repos > jjohnson > data_manager_hisat_index_builder
diff tool-data/hisat_indices.loc.sample @ 0:4c7db9cbbbf7 draft default tip
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| author | jjohnson |
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| date | Tue, 22 Jul 2014 08:52:53 -0400 (2014-07-22) |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hisat_indices.loc.sample Tue Jul 22 08:52:53 2014 -0400 @@ -0,0 +1,41 @@ +# hisat_indices.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 Bowtie2 and Tophat2. +# 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 hisat_indices.loc 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> +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/hisat/ +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r--. 1 galaxy galaxy 914M Jul 18 09:17 hg19canon.1.bt2 +# -rw-rw-r--. 1 galaxy galaxy 683M Jul 18 09:17 hg19canon.2.bt2 +# -rw-rw-r--. 1 galaxy galaxy 3.3K Jul 18 08:22 hg19canon.3.bt2 +# -rw-rw-r--. 1 galaxy galaxy 683M Jul 18 08:22 hg19canon.4.bt2 +# -rw-rw-r--. 1 galaxy galaxy 1.2G Jul 18 09:23 hg19canon.5.bt2 +# -rw-rw-r--. 1 galaxy galaxy 694M Jul 18 09:23 hg19canon.6.bt2 +# -rw-rw-r--. 2 galaxy galaxy 3.0G Nov 15 2011 hg19canon.fa +# -rw-rw-r--. 1 galaxy galaxy 914M Jul 18 10:13 hg19canon.rev.1.bt2 +# -rw-rw-r--. 1 galaxy galaxy 683M Jul 18 10:13 hg19canon.rev.2.bt2 +# -rw-rw-r--. 1 galaxy galaxy 1.2G Jul 18 10:20 hg19canon.rev.5.bt2 +# -rw-rw-r--. 1 galaxy galaxy 694M Jul 18 10:20 hg19canon.rev.6.bt2 +# +# then the hisat_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/hisat/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/hisat/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/hisat/dm3 +# +#