view rgweblogo/README @ 9:3af85bc54c8d draft

Uploaded

This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool
Last updated by Ross to install iuc ghostscript and numpy dependencies.

Weblogo generates sequence logos from fasta files such as the alignments generated by clustalw

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

**Automated Installation**
As a Galaxy admin, use the admin menu and select the search ToolShed option. This tool should be on the main toolshed - if not try the test toolshed.
Select it and choose "preview and install" - the process of downloading and installing weblogo3.3 and this wrapper should take a few minutes at most.

** Manual Installation**

Don't.

If you insist, 
Make sure weblogo3 is installed in your system python and is available on the path for all your nodes

Move the test data files to your galaxy root test-data
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.
Run
sh run_functional_tests.sh -id weblogo3
to make sure the tests work

then restart Galaxy and you should be good to go.


**Attribution**

Source for the weblogo3 python executable is at http://weblogo.berkeley.edu

Galaxy tool wrapper written by Ross Lazarus for the Rgenetics project

Copyright Ross Lazarus at gmail com 2011

All rights reserved.

Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html