view tools/nlstradamus/nlstradamus.txt @ 2:9ec94203d895 draft

Uploaded v0.0.7 with automatic installation of the C++ binary.

Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
=========================================================

This wrapper 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.

NLStradamus is a command line tools for predicting nuclear localization
signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).

A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
BMC Bioinformatics. 2009 Jun 29;10(1):202.
http://dx.doi.org/10.1186/1471-2105-10-202

http://www.moseslab.csb.utoronto.ca/NLStradamus

Early versions of NLStradamus did not have a native tabular output format, this
was added in version 1.7. Additionally a fast C++ implementation was added at
this point (early versions of NLStradamus came as a perl script only).

Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
unchanged.


Automated Installation
======================

This should be straightforward, Galaxy should automatically download and install
the C++ implementation of NLStradamus v1.8, and run the unit tests.


Manual Installation
===================
This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
PATH.

To install the wrapper copy or move the following files under the Galaxy tools
folder, e.g. in a tools/protein_analysis folder:

* nlstradamus.xml (the Galaxy tool definition)
* nlstradamus.txt (this README file)

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 (matching the chosen install path):

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

If you wish to run the unit tests, also add this to tools_conf.xml.sample
and move/copy the test-data files under Galaxy's test-data folder. Then:

$ ./run_functional_tests.sh -id nlstradamus

That's it.


History
=======

v0.0.3 - Initial public release
v0.0.4 - Adding DOI link to reference
         (Documentation change only)
v0.0.5 - Assume non-zero return codes are errors
v0.0.6 - Show output help text using a table
       - Added unit tests
v0.0.7 - Automatic installation of the NLStradamus binary when installed
         via the Galaxy Tool Shed


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 nlstradmus.tar.gz tools/nlstradamus/nlstradamus.xml tools/nlstradamus/nlstradamus.txt tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular

Check this worked:

$ tar -tzf nlstradmus.tar.gz
tools/nlstradamus/nlstradamus.xml
tools/nlstradamus/nlstradamus.txt
tools/nlstradamus/tool_dependencies.xml
test-data/four_human_proteins.fasta
test-data/four_human_proteins.nlstradamus.tabular
test-data/empty.fasta
test-data/empty_nlstradamus.tabular


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.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.

NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus
is is available and licenced separately (under the GPL v3 or later).