Mercurial > repos > devteam > cuffdiff

annotate tool-data/fasta_indexes.loc.sample @ 3:beab768feb92

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to the new data table specification.
author Dave Bouvier <dave@bx.psu.edu>
date Wed, 04 Dec 2013 13:24:38 -0500
parents
children 63b3133e535b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
2 #to use a directory of Samtools indexed sequences data files. You will need
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
3 #to create these data files and then create a sam_fa_new_indices.loc file
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
5 #the directories in which those files are stored. The sam_fa_new_indices.loc
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
7 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
9 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
10 #So, for example, if you had hg19 Canonical indexed stored in
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
11 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
12 # /depot/data2/galaxy/hg19/sam/,
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
13 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
14 #then the sam_fa_new_indices.loc entry would look like this:
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
15 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
17 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
18 #and your /depot/data2/galaxy/hg19/sam/ directory
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
19 #would contain hg19canon.fa and hg19canon.fa.fai files.
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
20 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
21 #Your sam_fa_new_indices.loc file should include an entry per line for
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
22 #each index set you have stored. The file in the path does actually
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
23 #exist, but it should never be directly used. Instead, the name serves
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
24 #as a prefix for the index file. For example:
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
25 #
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
beab768feb92 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa