view rgweblogo/README @ 3:78fe723fde78 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

It 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**

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

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