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+This package contains Galaxy wrappers for a selection of standalone command
+line protein analysis tools:
+
+* SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
+  Sequence Analysis at the Technical University of Denmark,
+  http://www.cbs.dtu.dk/cbs/
+
+* WoLF PSORT v0.2 from http://wolfpsort.org/
+
+* PSORTb v3 from http://www.psort.org/downloads/index.html
+
+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 (an MIT style 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 (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
+=======
+
+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
+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 $NSLOTS for thread count (otherwise default to 4)
+v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
+v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
+         contributed by Konrad Paszkiewicz.
+v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
+         files accidentally included previously via a wildcard).
+v0.2.2 - Include missing test files.
+v0.2.3 - Added unit tests for WoLF PSORT.
+v0.2.4 - Added unit tests for Promoter 2
+v0.2.5 - Link to Tool Shed added to help text and this documentation.
+       - More unit tests.
+       - Fixed bug with RXLR tool and empty FASTA files.
+       - Fixed typo in the RXLR tool help text.
+       - Updated citation information (Cock et al. 2013).
+
+
+Developers
+==========
+
+This script and other tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+This incorporates the previously used hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
+
+For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+$ ./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.