Mercurial > repos > devteam > cufflinks

annotate tool-data/fasta_indexes.loc.sample @ 13:6926716bbfb5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit 80b06e80066b32ad53ed418628992f056444256f
author iuc
date Sat, 05 Oct 2024 11:16:09 +0000
parents fe6f99e3d7f4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
da11bfc10e81 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
da11bfc10e81 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
5
fe6f99e3d7f4 Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 2
diff changeset
3 #to create these data files and then create a fasta_indexes.loc file
2
da11bfc10e81 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
5
fe6f99e3d7f4 Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 2
diff changeset
5 #the directories in which those files are stored. The fasta_indexes.loc
2
da11bfc10e81 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):
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
7 #
da11bfc10e81 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>
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
9 #
da11bfc10e81 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
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
11 #
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
12 # /depot/data2/galaxy/hg19/sam/,
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
13 #
5
fe6f99e3d7f4 Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 2
diff changeset
14 #then the fasta_indexes.loc entry would look like this:
2
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
15 #
da11bfc10e81 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
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
17 #
da11bfc10e81 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
da11bfc10e81 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.
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
20 #
5
fe6f99e3d7f4 Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 2
diff changeset
21 #Your fasta_indexes.loc file should include an entry per line for
2
da11bfc10e81 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
da11bfc10e81 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
da11bfc10e81 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:
da11bfc10e81 Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
25 #
da11bfc10e81 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
da11bfc10e81 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
da11bfc10e81 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
da11bfc10e81 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