Mercurial > repos > peterjc > nlstradamus
changeset 3:b2e648e55ed7 draft
Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub
| author | peterjc |
|---|---|
| date | Wed, 18 Sep 2013 06:15:33 -0400 |
| parents | 9ec94203d895 |
| children | 1458e60f3fd0 |
| files | tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.txt tools/nlstradamus/nlstradamus.xml |
| diffstat | 3 files changed, 143 insertions(+), 120 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/nlstradamus/README.rst Wed Sep 18 06:15:33 2013 -0400 @@ -0,0 +1,128 @@ +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.
--- a/tools/nlstradamus/nlstradamus.txt Tue Apr 23 11:59:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,116 +0,0 @@ -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).
--- a/tools/nlstradamus/nlstradamus.xml Tue Apr 23 11:59:14 2013 -0400 +++ b/tools/nlstradamus/nlstradamus.xml Wed Sep 18 06:15:33 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="nlstradamus" name="NLStradamus" version="0.0.7"> +<tool id="nlstradamus" name="NLStradamus" version="0.0.8"> <description>Find nuclear localization signals (NLSs) in protein sequences</description> <command> NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file @@ -71,12 +71,23 @@ **References** -A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses (2009). NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. -BMC Bioinformatics. 2009 Jun 29;10(1):202. +BMC Bioinformatics 10(1):202. http://dx.doi.org/10.1186/1471-2105-10-202 -http://www.moseslab.csb.utoronto.ca/NLStradamus +See also http://www.moseslab.csb.utoronto.ca/NLStradamus +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus </help> </tool>