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# pathoscope.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 Pathoscope_Map.
# 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.
#
# The path points to the "basename" for the set, not a specific file.
# It has four text columns seperated by TABS.
# <unique_build_id>	<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
#
#Important: put all reference bowtie index into same directory (including both
#target and filter reference botwie index)
#
#More examples:
#ref_prok_rep_genomes	prok	/depot/data/ref
#ce11	ce	/depot/data/ref