# bowtie2_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 bowtie_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. # # # # So, for example, if you had hg18 indexes stored in: # # /depot/data2/galaxy/hg19/bowtie2/ # # containing hg19 genome and hg19.*.bt2 files, such as: # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 # # then the bowtie2_indices.loc entry could look like this: # #hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon # #More examples: # #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 # #