annotate README @ 15:a6a92a8fe166 draft

Uploaded
author kevyin
date Mon, 12 Nov 2012 01:17:03 -0500
parents 1e428d8defbc
children c3e0e0a0ae09
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
1 Meme-chip wrapper for Galaxy
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
2
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
3 ========Installation instructions========:
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
4 First make sure meme is installed and accessible from the command line.
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
5 Meme-chip assumes the meme tools are in PATH.
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
6
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
7 ========Tool data table conf========
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
8 Check the entry is in tool_data_table_conf.xml
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
9
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
10 ========Tool loc file========
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
11
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
12 Example in tool-data/meme_chip_motifs.loc.sample
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
13 Entries come from the motif_db.csv in the motif database folder
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
14
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
15 make sure:
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
16 - 3 cols
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
17 - tab delimited
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
18 - paths are correct
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
19
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
20 There is a script to convert the csv to the loc format here:
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
21 https://bitbucket.org/gvl/meme-chip/src
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
22 After running delete the loc entries with multiple paths eg. All Vertebrates
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
23
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
24
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
25 LICENSE for this wrapper:
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
26 Kevin Ying
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
27 Garvan Institute http://www.garvan.org.au
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
28 GVL https://genome.edu.au/wiki/GVL
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
29
1e428d8defbc Uploaded
kevyin
parents:
diff changeset
30 http://opensource.org/licenses/mit-license.php