Mercurial > repos > bigrna > gpsrna
comparison tool-data/repeat_annotate.loc.sample @ 0:87fe81de0931 draft default tip
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| author | bigrna |
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| date | Sun, 04 Jan 2015 02:47:25 -0500 |
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| -1:000000000000 | 0:87fe81de0931 |
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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 # |