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/tool-data/bowtie_indices_color.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/
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 1#This is a sample file distributed with Galaxy that enables tools
 2#to use a directory of Bowtie indexed sequences data files. You will
 3#need to create these data files and then create a bowtie_indices.loc
 4#file similar to this one (store it in this directory) that points to
 5#the directories in which those files are stored. The bowtie_indices.loc
 6#file has this format (longer white space characters are TAB characters):
 7#
 8#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
 9#
10#So, for example, if you had hg18 indexed stored in 
11#/depot/data2/galaxy/bowtie/hg18/, 
12#then the bowtie_indices.loc entry would look like this:
13#
14#hg18   hg18   hg18   /depot/data2/galaxy/bowtie/hg18/hg18
15#
16#and your /depot/data2/galaxy/bowtie/hg18/ directory
17#would contain hg18.*.ebwt files:
18#
19#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
20#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
21#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
22#...etc...
23#
24#Your bowtie_indices.loc file should include an entry per line for each
25#index set you have stored. The "file" in the path does not actually
26#exist, but it is the prefix for the actual index files. For example:
27#
28#hg18canon          hg18   hg18 Canonical   /depot/data2/galaxy/bowtie/hg18/hg18canon
29#hg18full           hg18   hg18 Full        /depot/data2/galaxy/bowtie/hg18/hg18full
30#/orig/path/hg19    hg19   hg19             /depot/data2/galaxy/bowtie/hg19/hg19
31#...etc...
32#
33#Note that for backwards compatibility with workflows, the unique ID of
34#an entry must be the path that was in the original loc file, because that
35#is the value stored in the workflow for that parameter. That is why the
36#hg19 entry above looks odd. New genomes can be better-looking.
37#