mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
Kelly Vincent
30 lines
1.2 KiB
Plaintext
30 lines
1.2 KiB
Plaintext
#This is a sample file distributed with Galaxy that enables tools
|
|
#to use a directory of BWA indexed sequences data files. You will need
|
|
#to create these data files and then create a sequence_index_base.loc file
|
|
#similar to this one (store it in this directory) that points to
|
|
#the directories in which those files are stored. The sequence_index_base.loc
|
|
#file has this format (white space characters are TAB characters):
|
|
#
|
|
#<build> <file_base>
|
|
#
|
|
#So, for example, if you had phiX indexed stored in
|
|
#/depot/data2/galaxy/phiX/base/,
|
|
#then the sequence_index_base.loc entry would look like this:
|
|
#
|
|
#phiX /depot/data2/galaxy/phiX/base/phiX.fa
|
|
#
|
|
#and your /depot/data2/galaxy/phiX/base/ directory
|
|
#would contain phiX.fa.* files:
|
|
#
|
|
#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
|
|
#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
|
|
#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
|
|
#...etc...
|
|
#
|
|
#Your sequence_index_base.loc file should include an entry per line for
|
|
#each index set you have stored. The "file" in the path does not actually
|
|
#exist, but it is the prefix for the actual index files. For example:
|
|
#
|
|
#phiX /depot/data2/galaxy/phiX/base/phiX.fa
|
|
#hg18 /depot/data2/galaxy/hg18/base/hg18.fa
|