annotate tools/protein_analysis/README @ 11:99b82a2b1272 draft

Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)

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).

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 following test files (from these archive) to Galaxy
   subfolder test-data:

four_human_proteins.fasta
four_human_proteins_signalp3.tabular
four_human_proteins_tmhmm2.tabular
empty.fasta
empty_tmhmm2.tabular
empty_signalp3.tabular
k12_ten_proteins.fasta
k12_ten_proteins_psortb_p_terse.tabular

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.


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:

tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/psortb.xml tools/protein_analysis/psortb.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular test-data/k12_ten_proteins.fasta test-data/k12_ten_proteins_psortb_p_terse.tabular

Check this worked:

$ tar -tzf ~/tmhmm_signalp_etc.tar.gz
tools/protein_analysis/LICENSE
tools/protein_analysis/README
tools/protein_analysis/suite_config.xml
tools/protein_analysis/seq_analysis_utils.py
tools/protein_analysis/signalp3.xml
tools/protein_analysis/signalp3.py
tools/protein_analysis/tmhmm2.xml
tools/protein_analysis/tmhmm2.py
tools/protein_analysis/promoter2.xml
tools/protein_analysis/promoter2.py
tools/protein_analysis/psortb.xml
tools/protein_analysis/psortb.py
tools/protein_analysis/wolf_psort.xml
tools/protein_analysis/wolf_psort.py
tools/protein_analysis/rxlr_motifs.xml
tools/protein_analysis/rxrl_motifs.py
tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
test-data/four_human_proteins.fasta
test-data/four_human_proteins.signalp3.tabular
test-data/four_human_proteins.tmhmm2.tabular
test-data/empty.fasta
test-data/empty_tmhmm2.tabular
test-data/empty_signalp3.tabular
test-data/k12_ten_proteins.fasta
test-data/k12_ten_proteins_psortb_p_terse.tabular