Mercurial > repos > dongjun > csem
comparison bowtie_indices.loc.sample @ 3:3ce7ee6f43a7
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| author | dongjun |
|---|---|
| date | Mon, 12 Sep 2011 10:01:12 -0400 |
| parents | 3b583c9d06d4 |
| children |
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| 2:7796cbc040c4 | 3:3ce7ee6f43a7 |
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| 1 hg18 hg18 Human (Homo sapiens): hg18 /scratch/dongjun/galaxy/bowtie_indexes/ | |
| 2 mm9 mm9 Mouse (Mus musculus): mm9 /p/keles/SOFTWARE/bowtie-0.12.5/indexes/ | |
| 3 e_coli eschColi_536 Escherichia coli (str. 536) /p/keles/SOFTWARE/bowtie-0.12.5/indexes/ | |
| 4 e_coli_K12 eschColi_K12 Escherichia coli K12 (eschColi_K12) /scratch/dongjun/galaxy/bowtie_indexes/ | |
| 5 c_elegans_ws200 ce7 Caenorhabditis elegans (Feb 2009): WS200/ce7 /p/keles/SOFTWARE/bowtie-0.12.5/indexes/ | |
| 6 a_thaliana a_thaliana Arabidopsis thaliana /p/keles/SOFTWARE/bowtie-0.12.5/indexes/ | |
| 7 | |
| 8 #This is a sample file distributed with Galaxy that enables tools | |
| 9 #to use a directory of Bowtie indexed sequences data files. You will | |
| 10 #need to create these data files and then create a bowtie_indices.loc | |
| 11 #file similar to this one (store it in this directory) that points to | |
| 12 #the directories in which those files are stored. The bowtie_indices.loc | |
| 13 #file has this format (longer white space characters are TAB characters): | |
| 14 # | |
| 15 #<unique_build_id> <dbkey> <display_name> <file_base_path> | |
| 16 # | |
| 17 #So, for example, if you had hg18 indexed stored in | |
| 18 #/depot/data2/galaxy/bowtie/hg18/, | |
| 19 #then the bowtie_indices.loc entry would look like this: | |
| 20 # | |
| 21 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 | |
| 22 # | |
| 23 #and your /depot/data2/galaxy/bowtie/hg18/ directory | |
| 24 #would contain hg18.*.ebwt files: | |
| 25 # | |
| 26 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt | |
| 27 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt | |
| 28 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt | |
| 29 #...etc... | |
| 30 # | |
| 31 #Your bowtie_indices.loc file should include an entry per line for each | |
| 32 #index set you have stored. The "file" in the path does not actually | |
| 33 #exist, but it is the prefix for the actual index files. For example: | |
| 34 # | |
| 35 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon | |
| 36 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full | |
| 37 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 | |
| 38 #...etc... | |
| 39 # | |
| 40 #Note that for backwards compatibility with workflows, the unique ID of | |
| 41 #an entry must be the path that was in the original loc file, because that | |
| 42 #is the value stored in the workflow for that parameter. That is why the | |
| 43 #hg19 entry above looks odd. New genomes can be better-looking. | |
| 44 # |