comparison tools/protein_analysis/README @ 13:c6e5a737d3a0 draft

Uploaded v0.2.2, was missing some test files

12:7ef4b36b026a

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:

   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.

    <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

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
==========

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

13:c6e5a737d3a0

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:

   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.

    <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

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.


Developers
==========

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.