#This is a sample file distributed with Galaxy that enables tools #to use a directory of Bowtie indexed sequences data files. You will #need to create these data files and then create a bowtie_indices.loc #file similar to this one (store it in this directory) that points to #the directories in which those files are stored. The bowtie_indices.loc #file has this format (longer white space characters are TAB characters): # # # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, #then the bowtie_indices.loc entry would look like this: # #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt #...etc... # #Your bowtie_indices.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: # #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of #an entry must be the path that was in the original loc file, because that #is the value stored in the workflow for that parameter. That is why the #hg19 entry above looks odd. New genomes can be better-looking. #