# HG changeset patch # User eduardo # Date 1438358727 14400 # Node ID a44f024cb431f4b5f952ece261bee97500a267f2 # Parent 74888fd8e705a3425ef458e500512c91a1d66642 Uploaded diff -r 74888fd8e705 -r a44f024cb431 bowtie2_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie2_indices.loc.sample Fri Jul 31 12:05:27 2015 -0400 @@ -0,0 +1,750 @@ + + + + + + + + + + + + + tools-devteam/bowtie2_indices.loc.sample at master · galaxyproject/tools-devteam · GitHub + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
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# 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.
#
# <unique_build_id> <dbkey> <display_name> <file_base_path>
#
# 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
#
#
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