tmhmm_and_signalp: tools/protein_analysis/README annotate

annotate tools/protein_analysis/README @ 9:e52220a9ddad draft

Uploaded v0.1.2 Use the new <stdio> settings in the XML wrappers to catch errors. Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).

author	peterjc
date	Fri, 25 Jan 2013 06:08:31 -0500
parents	976a5f2833cd
children	09ff180d1615

rev	line source
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	1 This package contains Galaxy wrappers for a selection of standalone command
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	2 line protein analysis tools:
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	3
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	5 Sequence Analysis at the Technical University of Denmark,
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	6 http://www.cbs.dtu.dk/cbs/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	7
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	8 * WoLF PSORT v0.2 from http://wolfpsort.org/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	9
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	11
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	12 To use these Galaxy wrappers you must first install the command line tools.
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	13 At the time of writing they are all free for academic use.
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	14
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	15 These wrappers are copyright 2010-2012 by Peter Cock, James Hutton Institute
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	16 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	17 See the included LICENCE file for details (an MIT style open source licence).
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	19 Requirements
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	20 ============
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	21
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	22 First install those command line tools you wish to use the wrappers for:
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	23
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	24 1. Install the command line version of SignalP 3.0 and ensure "signalp" is
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	25 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	27 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	28 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	29
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	30 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	31 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	32
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	33 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	34 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	35 directory, run runWolfPsortSummary, and then change back to the original
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	36 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	37
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	38 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	39 but put it on the path under the name hmmsearch2 (allowing it to co-exist
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	40 with HMMER 3), or edit rlxr_motif.py accordingly.
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	41
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	42 Verify each of the tools is installed and working from the command line
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	43 (when logged in as the Galaxy user if appropriate).
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	44
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	45 Manual Installation
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	46 ===================
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	47
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	48 1. Create a folder tools/protein_analysis under your Galaxy installation.
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	49 This folder name is not critical, and can be changed if desired - you
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	50 must update the paths used in tool_conf.xml to match.
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	51
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	52 2. Copy/move the following files (from this archive) there:
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	53
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	54 tmhmm2.xml (Galaxy tool definition)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	55 tmhmm2.py (Python wrapper script)
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	56
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	57 signalp3.xml (Galaxy tool definition)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	58 signalp3.py (Python wrapper script)
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	59
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	60 promoter2.xml (Galaxy tool definition)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	61 promoter2.py (Python wrapper script)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	62
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	63 wolf_psort.xml (Galaxy tool definition)
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	64 wolf_psort.py (Python wrapper script)
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	65
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	66 rxlr_motifs.xml (Galaxy tool definition)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	67 rxlr_motifs.py (Python script)
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	68
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	69 seq_analysis_utils.py (shared Python code)
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	70 LICENCE
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	71 README (this file)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	72
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	73 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	74 also tool_conf.xml.sample (to run the tests) to include the new tools
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 by adding:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	76
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	77 <section name="Protein sequence analysis" id="protein_analysis">
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	78 <tool file="protein_analysis/tmhmm2.xml" />
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 <tool file="protein_analysis/signalp3.xml" />
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	80 <tool file="protein_analysis/wolf_psort.xml" />
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	81 <tool file="protein_analysis/rxlr_motifs.xml" />
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 </section>
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	83 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	84 <tool file="protein_analysis/promoter2.xml" />
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	85 </section>
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	86
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	87 Leave out the lines for any tools you do not wish to use in Galaxy.
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	88
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	89 4. Copy/move the following test files (from these archive) to Galaxy
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	90 subfolder test-data:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92 four_human_proteins.fasta
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	93 four_human_proteins_signalp3.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	94 four_human_proteins_tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	95 empty.fasta
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	96 empty_tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	97 empty_signalp3.tabular
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	98
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	99 5. Run the Galaxy functional tests for these new wrappers with:
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	101 ./run_functional_tests.sh -id tmhmm2
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	102 ./run_functional_tests.sh -id signalp3
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	104 Alternatively, this should work (assuming you left the name and id as shown in
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 the XML file tool_conf.xml.sample):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	107 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	109 6. Restart Galaxy and check the new tools are shown and work.
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	110
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	111
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	112 History
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	113 =======
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	114
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	115 v0.0.1 - Initial release
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	116 v0.0.2 - Corrected some typos in the help text
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	117 - Renamed test output file to use Galaxy convention of *.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	118 v0.0.3 - Check for tmhmm2 silent failures (no output)
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	119 - Additional unit tests
2 6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	120 v0.0.4 - Ignore comment lines in tmhmm2 output.
6901298ac16c Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository peterjc parents: 1 diff changeset	121 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
3 f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 2 diff changeset	122 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
4 81caef04ce8b Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	123 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
81caef04ce8b Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	124 SignalP webservice.
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	125 v0.0.8 - Added WoLF PSORT wrapper to the suite.
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	126 v0.0.9 - Added our RXLR motifs tool to the suite.
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
8 976a5f2833cd Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0 peterjc parents: 7 diff changeset	129 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
9 e52220a9ddad Uploaded v0.1.2 peterjc parents: 8 diff changeset	130 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
e52220a9ddad Uploaded v0.1.2 peterjc parents: 8 diff changeset	131 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
e52220a9ddad Uploaded v0.1.2 peterjc parents: 8 diff changeset	132
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	133
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	134 Developers
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	135 ==========
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	136
3 f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 2 diff changeset	137 This script and other tools are being developed on the following hg branch:
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 2 diff changeset	138 http://bitbucket.org/peterjc/galaxy-central/src/tools
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 2 diff changeset	139
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 2 diff changeset	140 This incorporates the previously used hg branch:
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	141 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	142
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	143 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	144 the following command from the Galaxy root folder:
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	145
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	146 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/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	147
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	148 Check this worked:
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	149
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	150 $ tar -tzf tmhmm_signalp_etc.tar.gz
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	151 tools/protein_analysis/LICENSE
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	152 tools/protein_analysis/README
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	153 tools/protein_analysis/suite_config.xml
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	154 tools/protein_analysis/seq_analysis_utils.py
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	155 tools/protein_analysis/signalp3.xml
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	156 tools/protein_analysis/signalp3.py
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	157 tools/protein_analysis/tmhmm2.xml
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	158 tools/protein_analysis/tmhmm2.py
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	159 tools/protein_analysis/promoter2.xml
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	160 tools/protein_analysis/promoter2.py
5 0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	161 tools/protein_analysis/wolf_psort.xml
0f1c61998b22 Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	162 tools/protein_analysis/wolf_psort.py
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	163 tools/protein_analysis/rxlr_motifs.xml
a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	164 tools/protein_analysis/rxrl_motifs.py
1 3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	165 test-data/four_human_proteins.fasta
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	166 test-data/four_human_proteins.signalp3.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	167 test-data/four_human_proteins.tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	168 test-data/empty.fasta
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	169 test-data/empty_tmhmm2.tabular
3ff1dcbb9440 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	170 test-data/empty_signalp3.tabular

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README @ 9:e52220a9ddad draft