mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
Dannon Baker
29 lines
1.5 KiB
Plaintext
29 lines
1.5 KiB
Plaintext
#This is a sample file distributed with Galaxy that enables tools to
|
|
#use a directory of PerM indexed sequences data files. You will need
|
|
#to create these data files and then create a perm_color_index.loc file
|
|
#similar to this one (store it in this directory) that points to
|
|
#the directories in which those files are stored. The perm_color_index.loc
|
|
#file has this format (white space characters are TAB characters):
|
|
#
|
|
#<build_seed_readlength> <display_name> <file_base>
|
|
#
|
|
#Because each PerM index is built with a specific seed and a specific read
|
|
#length, this needs to be specified so the user can choose the appropriate
|
|
#one. So, for example, if you had phiX indexed with seed F3 and read length
|
|
#50, and stored in /depot/data/galaxy/phiX/perm_index/,
|
|
#then the perm_color_index.loc entry would look something like this:
|
|
#
|
|
#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
|
|
#
|
|
#and your /depot/data/galaxy/phiX/perm_index/ directory
|
|
#would contain the file phiX_color_F3_50.index:
|
|
#
|
|
#Your perm_color_index.loc file should include an entry per line for each
|
|
#index set you have stored. For example:
|
|
#
|
|
#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
|
|
#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
|
|
#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
|
|
#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
|
|
#
|