Mercurial > repos > devteam > sam_to_bam
annotate tool-data/fasta_indexes.loc.sample @ 9:b77f7b516b17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author | iuc |
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date | Mon, 29 Jul 2019 08:47:05 -0400 |
parents | 05ca4081ca7e |
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rev | line source |
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93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
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1 #This is a sample file distributed with Galaxy that enables tools |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
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2 #to use a directory of Samtools indexed sequences data files. You will need |
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05ca4081ca7e
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents:
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3 #to create these data files and then create a fasta_indexes.loc file |
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93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
4 #similar to this one (store it in this directory) that points to |
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05ca4081ca7e
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents:
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diff
changeset
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5 #the directories in which those files are stored. The fasta_indexes.loc |
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93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
6 #file has this format (white space characters are TAB characters): |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
7 # |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
9 # |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
10 #So, for example, if you had hg19 Canonical indexed stored in |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
11 # |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
12 # /depot/data2/galaxy/hg19/sam/, |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
13 # |
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05ca4081ca7e
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents:
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14 #then the fasta_indexes.loc entry would look like this: |
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93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
15 # |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
17 # |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
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18 #and your /depot/data2/galaxy/hg19/sam/ directory |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
20 # |
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05ca4081ca7e
Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents:
1
diff
changeset
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21 #Your fasta_indexes.loc file should include an entry per line for |
1
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
22 #each index set you have stored. The file in the path does actually |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
23 #exist, but it should never be directly used. Instead, the name serves |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
24 #as a prefix for the index file. For example: |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
25 # |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
93f2e3337a33
Update sam_to_bam to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff
changeset
|
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |