https://github.com/galaxyproject/galaxy
Tip revision: 74eca3c953c6c99c3a5ccdc780c0ea273a5c305e authored by John Chilton on 15 October 2020, 16:15:17 UTC
Version 20.9.0 of web-framework (tag galaxy-web-framework-20.9.0).
Version 20.9.0 of web-framework (tag galaxy-web-framework-20.9.0).
Tip revision: 74eca3c
bfast_indexes.loc.sample
#This is a sample file distributed with Galaxy that enables tools
#to use a directory of BFAST indexed sequences data files. You will need
#to create these data files and then create a bfast_indices.loc file
#similar to this one (store it in this directory) that points to
#the directories in which those files are stored. The bfast_indexes.loc
#file has this format (white space characters are TAB characters):
#
#<unique_id> <build> <galaxy format extensions valid1,valid2> <description> <bfast_index_directory>
#
#
#So, for example, if you had hg18 indexed for 40+ bp NT reads stored in
#/galaxy/data/hg18/bfast_index/nt/40+,
#then the bfast_indices.loc entry could look like this:
#
#hg18_nt_40+ hg18 fastqsanger hg18: 40+ bp NT Space reads /galaxy/data/hg18/bfast_index/nt/40+/hg18.fa
#
#and your /depot/data2/galaxy/hg18/bfast/nt/40+ directory
#would contain hg18.fa.*.brg and hg18.fa.*.bif files:
#hg18.fa.nt.brg
#hg18.fa.nt.1.1.bif
#hg18.fa.nt.2.1.bif
#...etc...
#or similarly for color space indexes:
#hg18.fa.nt.brg #NB: the localalign process requires the nucleotide brg file
#hg18.fa.cs.brg
#hg18.fa.cs.1.1.bif
#hg18.fa.cs.2.1.bif
#...etc...
#
#a 'generic' directory can be used to hold intermixed NT and CS indexes, when differentiating is not needed, the bfast_indices.loc entry could look like this:
#hg18_standard hg18 fastqsanger,fastqcssanger hg18 standard indexes /galaxy/data/hg18/bfast_index/hg18.fa
#
#The use of symlinks to prevent copying of e.g. .fa and .brg files is recommended
#
#hg18_nt_40+ hg18 fastqsanger hg18: 40+ bp NT Space reads /galaxy/data/hg18/bfast_index/nt/40+/hg18.fa
#hg18_cs_50+ hg18 fastqcssanger hg18: 50+ bp Color space reads /galaxy/data/hg18/bfast_index/cs/50+/hg18.fa
#hg18_nt_40- hg18 fastqsanger hg18: 40- bp NT Space reads /galaxy/data/hg18/bfast_index/nt/40-/hg18.fa
#phiX_nt_50 phiX fastqsanger phiX: 50 bp NT Space reads /galaxy/data/phiX/bfast_index/nt/50/phiX.fa