Mercurial > repos > greg > gregs_test_repo
comparison galaxy_tmap_tool/tmap_index.loc.sample @ 14:8cfb224b440a
Uploaded galaxy_tmap_tool.tar
| author | greg |
|---|---|
| date | Thu, 21 Jul 2011 10:04:24 -0400 |
| parents | 09951b7d29a4 |
| children |
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| 13:4449cd364d3e | 14:8cfb224b440a |
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| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of TMAP indexed sequences data files. You will need | |
| 3 #to create these data files and then create a tmap_index.loc file | |
| 4 #similar to this one (store it in this directory) that points to | |
| 5 #the directories in which those files are stored. The tmap_index.loc | |
| 6 #file has this format (longer white space characters are TAB characters): | |
| 7 # | |
| 8 #<unique_build_id> <dbkey> <display_name> <file_path> | |
| 9 # | |
| 10 #So, for example, if you had phiX indexed stored in | |
| 11 #/depot/data2/galaxy/phiX/base/, | |
| 12 #then the tmap_index.loc entry would look like this: | |
| 13 # | |
| 14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa | |
| 15 # | |
| 16 #and your /depot/data2/galaxy/phiX/base/ directory | |
| 17 #would contain phiX.fa.* files: | |
| 18 # | |
| 19 #-rw-r--r-- 1 nilshomer staff 68B Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.anno | |
| 20 #-rw-r--r-- 1 nilshomer staff 172M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.bwt | |
| 21 #-rw-r--r-- 1 nilshomer staff 1.1M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.pac | |
| 22 #-rw-r--r-- 1 nilshomer staff 172M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.rbwt | |
| 23 #-rw-r--r-- 1 nilshomer staff 1.1M Jan 27 15:53 /data/mapping/genomes/DH10B/DH10B.fa.tmap.rpac | |
| 24 #-rw-r--r-- 1 nilshomer staff 572K Jan 27 15:54 /data/mapping/genomes/DH10B/DH10B.fa.tmap.rsa | |
| 25 #-rw-r--r-- 1 nilshomer staff 572K Jan 27 15:54 /data/mapping/genomes/DH10B/DH10B.fa.tmap.sa | |
| 26 #...etc... | |
| 27 # | |
| 28 #Your tmap_index.loc file should include an entry per line for each | |
| 29 #index set you have stored. The "file" in the path does not actually | |
| 30 #exist, but it is the prefix for the actual index files. For example: | |
| 31 # | |
| 32 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa | |
| 33 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa | |
| 34 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa | |
| 35 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa | |
| 36 #...etc... | |
| 37 # | |
| 38 #Note that for backwards compatibility with workflows, the unique ID of | |
| 39 #an entry must be the path that was in the original loc file, because that | |
| 40 #is the value stored in the workflow for that parameter. That is why the | |
| 41 #hg19 entry above looks odd. New genomes can be better-looking. | |
| 42 # |