Mercurial > repos > rnateam > segemehl
comparison tool-data/segemehl_indices.loc.sample @ 0:94926c35b6f3 draft
intial uploaded
| author | rnateam |
|---|---|
| date | Thu, 17 Oct 2013 04:07:29 -0400 |
| parents | |
| children | 468b59eae694 |
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| -1:000000000000 | 0:94926c35b6f3 |
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| 1 #This is a sample file that enables the segemehl mapper to find genome indices | |
| 2 #and database files. You will need to create these data files and then create | |
| 3 #a segemehl_indices.loc file similar to this one (store it in this directory) | |
| 4 #that points to the directories in which those files are stored. | |
| 5 #The segemehl_indices.loc file has this format (longer white space characters are TAB characters): | |
| 6 # | |
| 7 #<unique_build_id> <dbkey> <display_name> <file_base_path> | |
| 8 # | |
| 9 #So, for example, if you had hg18 indexed stored in | |
| 10 #/data/0/galaxy/segemehl/hg18/, | |
| 11 #then the segemehl_indices.loc entry would look like this: | |
| 12 # | |
| 13 #hg18 hg18 hg18 /data/0/galaxy/segemehl/hg18/chromosomes.fa /data/0/galaxy/segemehl/hg18/chromosomes.idx | |
| 14 # | |
| 15 #and your /data/0/galaxy/segemehl/hg18/ directory | |
| 16 #would contain hg18.*.ebwt files: | |
| 17 # | |
| 18 #-rw-r--r-- 1 bag bag 539833 2013-10-13 10:12 chromosomes.idx | |
| 19 #-rw-r--r-- 1 bag bag 342562 2013-10-13 10:12 chromosomes.fa | |
| 20 #...etc... | |
| 21 # | |
| 22 #Your segemehl_indices.loc file should include an entry per line for each | |
| 23 #index set you have stored. The "file" in the path does not actually | |
| 24 #exist, but it is the prefix for the actual index files. For example: | |
| 25 # | |
| 26 #hg18canon hg18 hg18 Canonical /data/0/galaxy/segemehl/hg18/chromosomes_can.fa /data/0/galaxy/segemehl/hg18/chromosomes_can.idx | |
| 27 #hg18full hg18 hg18 Full /data/0/galaxy/segemehl/hg18/chromosomes_full.fa /data/0/galaxy/segemehl/hg18/chromosomes_full.idx | |
| 28 #/orig/path/hg19 hg19 hg19 /data/0/galaxy/segemehl/hg19/chromosomes.fa /data/0/galaxy/segemehl/hg19/chromosomes.idx | |
| 29 #...etc... | |
| 30 # |