Mercurial > repos > peterjc > predictnls

Python re-implementation of predictNLS with Galaxy wrapper
==========================================================

This Galaxy tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below.

The tool consists of a Galaxy interface definition (predictnls.xml), and a Python
script (predictnls.py) which re-implements the command line tool predictNLS. This
should match the behaviour of predictNLS v1.0.20 (July 2011), the current latest
release from the Rost Lab, see http://rostlab.org and their paper:

Murat Cokol, Rajesh Nair, and Burkhard Rost.
Finding nuclear localization signals.
EMBO reports 1(5), 411–415, 2000
http://dx.doi.org/10.1093/embo-reports/kvd092

This wrapper is available from the Galaxy Tool Shed at
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp


Automatic Installation
======================

This Galaxy tool is self contained, and so should install automatically via the
Galaxy Tool Shed. See http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls


Manual Installation
===================

There are just four files which should be moved under the Galaxy tools folder,
e.g. in a tools/protein_analysis filter:

* predictlns.xml (the Galaxy tool definition)
* predictlns.py (the Python script)
* predictlns.txt (this README file)
* My_NLS_list (the default set of NLS motifs from the Rost Lab)

You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
tool. If you are using other protein analysis tools like TMHMM or SignalP, put
it next to them. Just add the line::

  <tool file="protein_analysis/predictnls.xml" />

If you want to run the unit tests, also add this to tool_conf.xml.sample, and
copy the test files under test-data, then run::

    ./run_functional_tests.sh -id predictnls

That's it.


History
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
v0.0.4  - Initial public release.
v0.0.5  - Treat non-zero return codes as errors.
v0.0.6  - Link to Tool Shed added to help text and this documentation.
        - Use reStructuredText for this README file.
        - Updated citation information (Cock et al. 2013).
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
======= ======================================================================


Developers
==========

This script and related tools are being developed on the following hg branch:
http://bitbucket.org/peterjc/galaxy-central/src/tools

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder::

    $ tar -czf predictnls.tar.gz tools/predictnls/README.rst tools/predictnls/predictnls.xml tools/predictnls/predictnls.py tools/predictnls/My_NLS_list test-data/four_human_proteins.fasta test-data/four_human_proteins.predictnls.tabular

Check this worked::

    $ tar -tzf predictnls.tar.gz
    tools/predictnls/README.rst
    tools/predictnls/predictnls.xml
    tools/predictnls/predictnls.py
    tools/predictnls/My_NLS_list
    test-data/four_human_proteins.fasta
    test-data/four_human_proteins.predictnls.tabular


Licence (GPL)
=============

This tool is open source, licensed under the GNU GENERAL PUBLIC LICENSE
version 3 (GNU v3), see http://www.gnu.org/licenses/gpl.html

The Python script is my reimplementation of the original Perl program from
the Rost Lab, which was released under the GPL v3. Therefore, as I consider
this to be a derivative work, this too is released under the GPL v3.

Please note that the My_NLS_list should be an exact copy of the file of the
same name included with predictnls-1.0.7.tar.gz to predictnls-1.0.20.tar.gz
inclusive (the list was extended in v1.0.7 in August 2010, see the change log
included in those tar-balls), available from ftp://rostlab.org/predictnls/
author	peterjc
date	Fri, 11 Oct 2013 04:35:15 -0400
parents
children	9f2088ca5f6a