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Repository 'tmhmm_and_signalp'
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb
Galaxy wrappers for several standalone command line sequence analysis tools:

SignalP 3.0 predicts signal peptides, see:
http://www.cbs.dtu.dk/services/SignalP/

TMHMM 2.0 predicts transmembrane helices, see:
http://www.cbs.dtu.dk/services/TMHMM/

Promoter 2.0 predicts eukaryotic PolII promoters, see:
http://www.cbs.dtu.dk/services/Promoter/

WoLF PSORT predicts eukaryote protein sub-cellular localization, see:
http://wolfpsort.org/

POSRTb predicts prokaryote protein sub-cellular localization, see:
http://www.psort.org/documentation/index.html

Oomycete RXLR motif prediction - a Python script implementing three published methods, which calls SignalP 3.0 and HMMER 2.3.2 internally.

To use these Galaxy wrappers you must first install the command line tools, which at the the time of writing are all free for academic use or open source.

These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute (formerly SCRI), UK. All rights reserved.
Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved

The wrappers are released under a MIT style open source licence, see the included LICENCE file for details.
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peterjc
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Repository README files - may contain important installation or license information

This package contains Galaxy wrappers for a selection of standalone command line protein analysis tools:

Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.

To use these Galaxy wrappers you must first install the command line tools. At the time of writing they are all free for academic use, or open source.

These wrappers are copyright 2010-2013 by Peter Cock, James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved. See the included LICENCE file for details (MIT open source licence).

The wrappers are available from the Galaxy Tool Shed http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

Citation

If you use any of these Galaxy tools in work leading to a scientific publication, in addition to citing the invididual underlying tools, please cite:

Peter Cock, Bjoern Gruening, 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

Full reference information is included in the help text for each tool.

Requirements

First install those command line tools you wish to use the wrappers for:

  1. Install the command line version of SignalP 3.0 and ensure "signalp" is on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
  2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
  3. Install the command line version of Promoter 2.0 and ensure "promoter" is on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
  4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary" is on the PATH (we use an extra wrapper script to change to the WoLF PSORT directory, run runWolfPsortSummary, and then change back to the original directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
  5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2) but put it on the path under the name hmmsearch2 (allowing it to co-exist with HMMER 3), or edit rlxr_motif.py accordingly.

Verify each of the tools is installed and working from the command line (when logged in as the Galaxy user if appropriate).

Manual Installation

  1. Create a folder tools/protein_analysis under your Galaxy installation. This folder name is not critical, and can be changed if desired - you must update the paths used in tool_conf.xml to match.

  2. Copy/move the following files (from this archive) there:

    • tmhmm2.xml (Galaxy tool definition)
    • tmhmm2.py (Python wrapper script)
    • signalp3.xml (Galaxy tool definition)
    • signalp3.py (Python wrapper script)
    • promoter2.xml (Galaxy tool definition)
    • promoter2.py (Python wrapper script)
    • psortb.xml (Galaxy tool definition)
    • psortb.py (Python wrapper script)
    • wolf_psort.xml (Galaxy tool definition)
    • wolf_psort.py (Python wrapper script)
    • rxlr_motifs.xml (Galaxy tool definition)
    • rxlr_motifs.py (Python script)
    • seq_analysis_utils.py (shared Python code)
    • LICENCE
    • README.rst (this file)
  3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND also tool_conf.xml.sample (to run the tests) to include the new tools by adding:

    <section name="Protein sequence analysis" id="protein_analysis">
      <tool file="protein_analysis/tmhmm2.xml" />
      <tool file="protein_analysis/signalp3.xml" />
      <tool file="protein_analysis/psortb.xml" />
      <tool file="protein_analysis/wolf_psort.xml" />
      <tool file="protein_analysis/rxlr_motifs.xml" />
    </section>
    <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
      <tool file="protein_analysis/promoter2.xml" />
    </section>
    

    Leave out the lines for any tools you do not wish to use in Galaxy.

  4. Copy/move the test-data files (from this archive) to Galaxy's subfolder test-data.

  5. Run the Galaxy functional tests for these new wrappers with:

    ./run_functional_tests.sh -id tmhmm2
    ./run_functional_tests.sh -id signalp3
    ./run_functional_tests.sh -id Psortb
    ./run_functional_tests.sh -id rxlr_motifs
    

    Alternatively, this should work (assuming you left the name and id as shown in the XML file tool_conf.xml.sample):

    ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
    

    To check the section ID expected, use ./run_functional_tests.sh -list

  6. Restart Galaxy and check the new tools are shown and work.

History

Version Changes
v0.0.1
  • Initial release
v0.0.2
  • Corrected some typos in the help text

  • Renamed test output file to use Galaxy convention of *.tabular

    System Message: WARNING/2 (<string>, line 143); backlink

    Inline emphasis start-string without end-string.

v0.0.3
  • Check for tmhmm2 silent failures (no output)
  • Additional unit tests
v0.0.4
  • Ignore comment lines in tmhmm2 output.
v0.0.5
  • Explicitly request tmhmm short output (may not be the default)
v0.0.6
  • Improvement to how sub-jobs are run (should be faster)
v0.0.7
  • Change SignalP default truncation from 60 to 70 to match the SignalP webservice.
v0.0.8
  • Added WoLF PSORT wrapper to the suite.
v0.0.9
  • Added our RXLR motifs tool to the suite.
v0.1.0
  • Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
  • Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
v0.1.1
  • Fixed an error in the header of the tabular output from Promoter
v0.1.2
  • Use the new <stdio> settings in the XML wrappers to catch errors
  • Use SGE style $NSLOTS for thread count (otherwise default to 4)
v0.1.3
  • Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
v0.2.0
  • Added PSORTb wrapper to the suite, based on earlier work contributed by Konrad Paszkiewicz.
v0.2.1
  • Use a script to create the Tool Shed tar-ball (removed some stray files accidentally included previously via a wildcard).
v0.2.2
  • Include missing test files.
v0.2.3
  • Added unit tests for WoLF PSORT.
v0.2.4
  • Added unit tests for Promoter 2
v0.2.5
  • Link to Tool Shed added to help text and this documentation.
  • More unit tests.
  • Fixed bug with RXLR tool and empty FASTA files.
  • Fixed typo in the RXLR tool help text.
  • Updated citation information (Cock et al. 2013).
  • Adopted standard MIT licence.
  • Use reStructuredText for this README file.
  • Development moved to GitHub, https://github.com/peterjc/pico_galaxy

Developers

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

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

$ ./tools/protein_analysis/make_tmhmm_and_signalp.sh

This simplifies ensuring a consistent set of files is bundled each time, including all the relevant test files.

Contents of this repository

Name Description Version
psortb Determines sub-cellular localisation of bacterial/archaeal protein sequences 0.0.3
RXLR Motifs Find RXLR Effectors of Plant Pathogenic Oomycetes 0.0.7
TMHMM 2.0 Find transmembrane domains in protein sequences 0.0.11
WoLF PSORT Eukaryote protein subcellular localization prediction 0.0.6
SignalP 3.0 Find signal peptides in protein sequences 0.0.12
Promoter 2.0 Find eukaryotic PolII promoters in DNA sequences 0.0.6

Categories
Sequence Analysis