Mercurial > repos > matthias > samtools_depth
comparison bam_to_cram/tool-data/fasta_indexes.loc.sample @ 0:fe46361a85db draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
| author | matthias |
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| date | Fri, 22 Feb 2019 16:06:58 -0500 |
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| -1:000000000000 | 0:fe46361a85db |
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| 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 | |
| 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 | |
| 5 #the directories in which those files are stored. The fasta_indexes.loc | |
| 6 #file has this format (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 hg19 Canonical indexed stored in | |
| 11 # | |
| 12 # /depot/data2/galaxy/hg19/sam/, | |
| 13 # | |
| 14 #then the fasta_indexes.loc entry would look like this: | |
| 15 # | |
| 16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa | |
| 17 # | |
| 18 #and your /depot/data2/galaxy/hg19/sam/ directory | |
| 19 #would contain hg19canon.fa and hg19canon.fa.fai files. | |
| 20 # | |
| 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 | |
| 23 #exist, but it should never be directly used. Instead, the name serves | |
| 24 #as a prefix for the index file. For example: | |
| 25 # | |
| 26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa | |
| 27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa | |
| 28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa | |
| 29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |