Mercurial > repos > devteam > cufflinks
comparison tool-data/fasta_indexes.loc.sample @ 5:fe6f99e3d7f4 draft
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
| author | devteam |
|---|---|
| date | Thu, 09 Jan 2014 14:28:13 -0500 |
| parents | da11bfc10e81 |
| children |
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| 4:398329a94c99 | 5:fe6f99e3d7f4 |
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| 1 #This is a sample file distributed with Galaxy that enables tools | 1 #This is a sample file distributed with Galaxy that enables tools |
| 2 #to use a directory of Samtools indexed sequences data files. You will need | 2 #to use a directory of Samtools indexed sequences data files. You will need |
| 3 #to create these data files and then create a sam_fa_new_indices.loc file | 3 #to create these data files and then create a fasta_indexes.loc file |
| 4 #similar to this one (store it in this directory) that points to | 4 #similar to this one (store it in this directory) that points to |
| 5 #the directories in which those files are stored. The sam_fa_new_indices.loc | 5 #the directories in which those files are stored. The fasta_indexes.loc |
| 6 #file has this format (white space characters are TAB characters): | 6 #file has this format (white space characters are TAB characters): |
| 7 # | 7 # |
| 8 # <unique_build_id> <dbkey> <display_name> <file_base_path> | 8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
| 9 # | 9 # |
| 10 #So, for example, if you had hg19 Canonical indexed stored in | 10 #So, for example, if you had hg19 Canonical indexed stored in |
| 11 # | 11 # |
| 12 # /depot/data2/galaxy/hg19/sam/, | 12 # /depot/data2/galaxy/hg19/sam/, |
| 13 # | 13 # |
| 14 #then the sam_fa_new_indices.loc entry would look like this: | 14 #then the fasta_indexes.loc entry would look like this: |
| 15 # | 15 # |
| 16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa | 16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
| 17 # | 17 # |
| 18 #and your /depot/data2/galaxy/hg19/sam/ directory | 18 #and your /depot/data2/galaxy/hg19/sam/ directory |
| 19 #would contain hg19canon.fa and hg19canon.fa.fai files. | 19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
| 20 # | 20 # |
| 21 #Your sam_fa_new_indices.loc file should include an entry per line for | 21 #Your fasta_indexes.loc file should include an entry per line for |
| 22 #each index set you have stored. The file in the path does actually | 22 #each index set you have stored. The file in the path does actually |
| 23 #exist, but it should never be directly used. Instead, the name serves | 23 #exist, but it should never be directly used. Instead, the name serves |
| 24 #as a prefix for the index file. For example: | 24 #as a prefix for the index file. For example: |
| 25 # | 25 # |
| 26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa | 26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa |