On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:


Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to make this kind of documentation
more visible...


If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the "tool panel section selection page".  An example using the antismash repository on the main tool shed is below.  This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository.  It will be available in the next Galaxy distribution.

Care must be taken when following instructions in README files since some of the information may be outdated.  For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary.


Installation may take a while, depending upon the size of the repository contents. Wait until a message is displayed in your browser after clicking the Install button below.

Choose the tool panel section to contain the installed tools (optional)
Your Galaxy instance is configured with 1 shed tool configuration files, so choose one in which to configure the installed tools.
Add a new tool panel section to contain the installed tools (optional).
Choose an existing section in your tool panel to contain the installed tools (optional).
Clicking Install without selecting a tool panel section will load the installed tools into the tool panel outside of any sections.
Repository README file (may contain important installation or license information)
Galaxy wrapper for AntiSmash
=====================================

This wrapper is copyright 2012 by BjXXrn GrXXning.

This is a wrapper for the command line tool of antiSMASH.

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
It integrates and cross-links with a large number of in silico secondary metabolite analysis tools.

http://antismash.secondarymetabolites.org/

Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011).
antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.


Installation
============

Currently these wrapper is tested with version 1.1 and the modified version of antismash.py included in that repository.

Install or downlaod antiSMASH from:

http://antismash.secondarymetabolites.org/download.html

... and follow the instructions.
Please replace the antismash.py file with the one inlcuded in that repository.
Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation.

blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'


To install the wrapper copy the antiSMASH folder in the galaxy tools
folder and modify the tools_conf.xml file to make the tool available to Galaxy.
For example:

<section name="PKS-NRPS prediction" id="pks-nrps_prediction">
    <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" />
    <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" />
</section>


History
=======

v0.1 - Initial public release


Wrapper Licence (MIT/BSD style)
===============================

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

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WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.