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Repository 'nlstradamus'
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
nlstradamus
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Find nuclear localization signals (NLSs) in protein sequences
Wraps the NLStradamus tool for prediction of nuclear localization signals (NLSs), which uses a Hidden Markov Model (HMM).

Takes a FASTA file of proteins as input, returns a tabular file as output.

Requires the C++ version of NLStradamus, included with NLStradamus 1.7 (or later). See:

http://www.moseslab.csb.utoronto.ca/NLStradamus
3:b2e648e55ed7
peterjc
True
264

Repository README files - may contain important installation or license information

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 (MIT licence).

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

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

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

Version Changes
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
v0.0.8
  • Link to Tool Shed added to help text and this documentation.
  • Use reStructuredText for this README file.
  • Adopted standard MIT licence.
  • 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

Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus

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/README.rst tools/nlstradamus/nlstradamus.xml 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/README.rst
tools/nlstradamus/nlstradamus.xml
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)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Dependencies of this repository

Name Version Type
NLStradamus 1.8 package

Contents of this repository

Name Description Version
NLStradamus Find nuclear localization signals (NLSs) in protein sequences 0.0.8

Automated tool test results

Time tested: 2014-04-17 05:44:26
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
TypeNameVersion
NLStradamus package 1.8
Installation directory
/ToolDepsMain/NLStradamus/1.8/peterjc/nlstradamus/b2e648e55ed7
Time tested: 2014-04-16 05:38:47
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
TypeNameVersion
NLStradamus package 1.8
Installation directory
/ToolDepsMain/NLStradamus/1.8/peterjc/nlstradamus/b2e648e55ed7
Time tested: 2014-04-15 06:13:22
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
TypeNameVersion
NLStradamus package 1.8
Installation directory
/ToolDepsMain/NLStradamus/1.8/peterjc/nlstradamus/b2e648e55ed7
Time tested: 2014-04-14 05:35:47
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
TypeNameVersion
NLStradamus package 1.8
Installation directory
/ToolDepsMain/NLStradamus/1.8/peterjc/nlstradamus/b2e648e55ed7

Categories
Sequence Analysis
Fasta Manipulation