Mercurial > repos > devteam > cuffcompare
annotate tool-data/fasta_indexes.loc.sample @ 4:cf928aeaaff7
Merge heads.
author | Dave Bouvier <dave@bx.psu.edu> |
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date | Wed, 08 Jan 2014 09:16:52 -0500 |
parents | 8b22e9adae34 |
children | 67695d7ff787 |
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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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3 #to create these data files and then create a sam_fa_new_indices.loc file |
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4 #similar to this one (store it in this directory) that points to |
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5 #the directories in which those files are stored. The sam_fa_new_indices.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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14 #then the sam_fa_new_indices.loc entry would look like this: |
8b22e9adae34
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parents:
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15 # |
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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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18 #and your /depot/data2/galaxy/hg19/sam/ directory |
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19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
1 | 20 # |
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parents:
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21 #Your sam_fa_new_indices.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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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa |
8b22e9adae34
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parents:
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa |
8b22e9adae34
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Dave Bouvier <dave@bx.psu.edu>
parents:
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
8b22e9adae34
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parents:
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |