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comparison README @ 16:c3e0e0a0ae09 draft

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author kevyin
date Mon, 12 Nov 2012 19:34:55 -0500
parents 1e428d8defbc
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15:a6a92a8fe166 16:c3e0e0a0ae09
1 Meme-chip wrapper for Galaxy 1 Meme-chip wrapper for Galaxy
2 2
3 =========================================:
3 ========Installation instructions========: 4 ========Installation instructions========:
4 First make sure meme is installed and accessible from the command line. 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
5 Meme-chip assumes the meme tools are in PATH. 11 Meme-chip assumes the meme tools are in PATH.
12 Make sure meme is accessible
13
6 14
7 ========Tool data table conf======== 15 ========Tool data table conf========
8 Check the entry is in tool_data_table_conf.xml 16 Check the meme_chip_motifs entry is in tool_data_table_conf.xml
9 17
10 ========Tool loc file======== 18 ========Tool loc file========
11 19
12 Example in tool-data/meme_chip_motifs.loc.sample 20 Example in tool-data/meme_chip_motifs.loc.sample
13 Entries come from the motif_db.csv in the motif database folder 21 Entries come from the motif_db.csv in the motif database folder
20 There is a script to convert the csv to the loc format here: 28 There is a script to convert the csv to the loc format here:
21 https://bitbucket.org/gvl/meme-chip/src 29 https://bitbucket.org/gvl/meme-chip/src
22 After running delete the loc entries with multiple paths eg. All Vertebrates 30 After running delete the loc entries with multiple paths eg. All Vertebrates
23 31
24 32
33 =========================================:
25 LICENSE for this wrapper: 34 LICENSE for this wrapper:
35 =========================================:
26 Kevin Ying 36 Kevin Ying
27 Garvan Institute http://www.garvan.org.au 37 Garvan Institute: http://www.garvan.org.au
28 GVL https://genome.edu.au/wiki/GVL 38 GVL: https://genome.edu.au/wiki/GVL
29 39
30 http://opensource.org/licenses/mit-license.php 40 http://opensource.org/licenses/mit-license.php