Mercurial > repos > kevyin > meme_chip
comparison README @ 18:2948554ae3d7 draft default tip
added nmeme option
| author | kevyin |
|---|---|
| date | Thu, 22 Nov 2012 20:27:29 -0500 |
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| 17:5bb9eb050e57 | 18:2948554ae3d7 |
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| 1 Meme-chip wrapper for Galaxy | |
| 2 | |
| 3 =========================================: | |
| 4 ========Installation instructions========: | |
| 5 =========================================: | |
| 6 The tool_dependencies.xml can attempt to install meme in a folder specific for this tool. | |
| 7 (such as bwa_wrappers) | |
| 8 | |
| 9 The procedure does NOT download motif databases you will need to download them yourself | |
| 10 | |
| 11 Meme-chip assumes the meme tools are in PATH. | |
| 12 Make sure meme is accessible | |
| 13 | |
| 14 | |
| 15 ========Tool data table conf======== | |
| 16 Check the meme_chip_motifs entry is in tool_data_table_conf.xml | |
| 17 | |
| 18 ========Tool loc file======== | |
| 19 | |
| 20 Example in tool-data/meme_chip_motifs.loc.sample | |
| 21 Entries come from the motif_db.csv in the motif database folder | |
| 22 | |
| 23 make sure: | |
| 24 - 3 cols | |
| 25 - tab delimited | |
| 26 - paths are correct | |
| 27 | |
| 28 There is a script to convert the csv to the loc format here: | |
| 29 https://bitbucket.org/gvl/meme-chip/src | |
| 30 After running delete the loc entries with multiple paths eg. All Vertebrates | |
| 31 | |
| 32 | |
| 33 =========================================: | |
| 34 LICENSE for this wrapper: | |
| 35 =========================================: | |
| 36 Kevin Ying | |
| 37 Garvan Institute: http://www.garvan.org.au | |
| 38 GVL: https://genome.edu.au/wiki/GVL | |
| 39 | |
| 40 http://opensource.org/licenses/mit-license.php |