Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

annotate tool-data/deepTools_seqs.loc.sample @ 23:f8cd2985bc05 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit beb75870e99ed8ceca69753bf7de546877b3e2ff
author bgruening
date Fri, 12 Aug 2016 05:09:56 -0400
parents 49ff082ba574
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
2 #to use a directory of 2bit genome files for use with deepTools. You will
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
3 #need to supply these files and then create a deepTools_seqs.loc file
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
4 #similar to this one (store it in this directory) that points to
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
5 #the directories in which those files are stored. The deepTools_seqs.loc
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
6 #file has this format:
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
7 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
8 #<unique_build_id> <display_name> <file_path>
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
9 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
10 #So, for example, if your deepTools_seqs.loc began like this:
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
11 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
15 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
16 #then your /depot/data2/galaxy/twobit/ directory
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
17 #would need to contain the following 2bit files:
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
18 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
22 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
23 #Your deepTools_seqs.loc file should include an entry per line for
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
24 #each file you have stored that you want to be available. Note that
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
25 #your files should all have the extension '2bit'.
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
26 #
49ff082ba574 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty
bgruening
parents:
diff changeset
27 #Please note that the <unique_build_id> is also used as "Species name abbreviation".