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

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

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+++ b/tools/nlstradamus/nlstradamus.txt	Tue Apr 23 11:59:14 2013 -0400
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+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).