Mercurial > repos > devteam > cuffcompare
annotate tool-data/fasta_indexes.loc.sample @ 7:b77178f66fc3 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:34:16 -0500 |
| parents | 67695d7ff787 |
| children |
| rev | line source |
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| 1 | 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 | |
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67695d7ff787
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
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3 #to create these data files and then create a fasta_indexes.loc file |
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8b22e9adae34
Update to the new data table specification.
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4 #similar to this one (store it in this directory) that points to |
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67695d7ff787
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
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5 #the directories in which those files are stored. The fasta_indexes.loc |
| 1 | 6 #file has this format (white space characters are TAB characters): |
| 7 # | |
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
| 1 | 9 # |
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10 #So, for example, if you had hg19 Canonical indexed stored in |
| 1 | 11 # |
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12 # /depot/data2/galaxy/hg19/sam/, |
| 1 | 13 # |
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67695d7ff787
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14 #then the fasta_indexes.loc entry would look like this: |
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8b22e9adae34
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
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diff
changeset
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15 # |
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8b22e9adae34
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
| 1 | 17 # |
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parents:
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18 #and your /depot/data2/galaxy/hg19/sam/ directory |
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8b22e9adae34
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
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changeset
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19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
| 1 | 20 # |
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67695d7ff787
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents:
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diff
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21 #Your fasta_indexes.loc file should include an entry per line for |
| 1 | 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 # | |
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parents:
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa |
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8b22e9adae34
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Dave Bouvier <dave@bx.psu.edu>
parents:
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa |
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8b22e9adae34
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
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diff
changeset
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
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8b22e9adae34
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
1
diff
changeset
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |