Mercurial > repos > fubar > weblogo3
comparison rgweblogo/README @ 0:cec2527697f6
Migrated tool version 0.1 from old tool shed archive to new tool shed repository
| author | fubar |
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| date | Tue, 07 Jun 2011 17:43:58 -0400 |
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| -1:000000000000 | 0:cec2527697f6 |
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| 1 This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool | |
| 2 | |
| 3 It generates sequence logos from fasta files such as the alignments generated by clustalw | |
| 4 | |
| 5 Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data | |
| 6 | |
| 7 **Installation** | |
| 8 | |
| 9 Make sure weblogo3 is installed in your system python and is available on the path for all your nodes | |
| 10 | |
| 11 Move the test data files to your galaxy root test-data | |
| 12 Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there. | |
| 13 Run | |
| 14 sh run_functional_tests.sh -id weblogo3 | |
| 15 to make sure the tests work | |
| 16 | |
| 17 then restart Galaxy and you should be good to go. | |
| 18 | |
| 19 | |
| 20 **Attribution** | |
| 21 | |
| 22 Source for the weblogo3 python executable is at http://weblogo.berkeley.edu | |
| 23 | |
| 24 Written by Ross Lazarus for the Rgenetics project | |
| 25 | |
| 26 Copyright Ross Lazarus at gmail com 2011 | |
| 27 | |
| 28 All rights reserved. | |
| 29 | |
| 30 Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html |