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comparison tool-data/fasta_indexes.loc.sample @ 2:05ca4081ca7e

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Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
author devteam
date Thu, 09 Jan 2014 14:29:01 -0500
parents 93f2e3337a33
children
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1:93f2e3337a33 2:05ca4081ca7e
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