tmhmm_and_signalp: tools/protein_analysis/README annotate

annotate tools/protein_analysis/README @ 7:5e62aefb2918 draft

Uploaded v0.1.2 to Test Tool Shed

author	peterjc
date	Tue, 26 Mar 2013 14:24:56 -0400
parents	39a6e46cdda3
children	391a142c1e60

rev	line source
5 ef7ceca37e3f 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
ef7ceca37e3f 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:
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	3
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
5 ef7ceca37e3f 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,
ef7ceca37e3f 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/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	7
ef7ceca37e3f 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/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	9
6 39a6e46cdda3 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.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	11
5 ef7ceca37e3f 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.
ef7ceca37e3f 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.
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	14
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	15 These wrappers are copyright 2010-2012 by Peter Cock, James Hutton Institute
5 ef7ceca37e3f 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 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	17 See the included LICENCE file for details (an MIT style open source licence).
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18
5 ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	19 Requirements
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	20 ============
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	21
ef7ceca37e3f 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:
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	23
ef7ceca37e3f 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
ef7ceca37e3f 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26
5 ef7ceca37e3f 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
ef7ceca37e3f 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/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	29
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	30 3. Install the command line version of Promoter 2.0 and ensure "promoter" is
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	31 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	32
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	33 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
5 ef7ceca37e3f 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
ef7ceca37e3f 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
ef7ceca37e3f 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/
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	37
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	38 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
6 39a6e46cdda3 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
39a6e46cdda3 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.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	41
5 ef7ceca37e3f 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 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	43 (when logged in as the Galaxy user if appropriate).
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	44
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	45 Manual Installation
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	46 ===================
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	47
5 ef7ceca37e3f 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 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	49 This folder name is not critical, and can be changed if desired - you
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	50 must update the paths used in tool_conf.xml to match.
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	51
5 ef7ceca37e3f 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	53
a2eeeaa6f75e 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)
a2eeeaa6f75e 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 ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	56
0 a2eeeaa6f75e 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)
a2eeeaa6f75e 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 ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	59
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	60 promoter2.xml (Galaxy tool definition)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	61 promoter2.py (Python wrapper script)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	62
5 ef7ceca37e3f 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)
ef7ceca37e3f 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)
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	65
6 39a6e46cdda3 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)
39a6e46cdda3 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)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 5 diff changeset	68
0 a2eeeaa6f75e 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 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	70 LICENCE
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	71 README (this file)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	72
5 ef7ceca37e3f 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
ef7ceca37e3f 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 by adding:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	76
a2eeeaa6f75e 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">
a2eeeaa6f75e 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" />
a2eeeaa6f75e 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 ef7ceca37e3f 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 39a6e46cdda3 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 </section>
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	83 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	84 <tool file="protein_analysis/promoter2.xml" />
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	85 </section>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	86
5 ef7ceca37e3f 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.
ef7ceca37e3f Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	88
ef7ceca37e3f 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	90 subfolder test-data:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91
a2eeeaa6f75e 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 9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	95 empty.fasta
9a8a7f680dd6 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
9a8a7f680dd6 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	98
5 ef7ceca37e3f 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 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100
a2eeeaa6f75e 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
a2eeeaa6f75e 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
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103
a2eeeaa6f75e 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
a2eeeaa6f75e 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):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106
a2eeeaa6f75e 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
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108
5 ef7ceca37e3f 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 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	110
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	111
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	112 History
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	113 =======
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	114
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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)
9a8a7f680dd6 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 747cec3192d3 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.
747cec3192d3 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 fe10f448d641 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 1426b2bae76d 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
1426b2bae76d 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 ef7ceca37e3f 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 39a6e46cdda3 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 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	129 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	130 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	131 - Use SGE style $NSLOTS for thread count (otherwise default to 4)
4 1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	132
1 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	133
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	134 Developers
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	135 ==========
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	136
3 fe10f448d641 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:
fe10f448d641 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
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 2 diff changeset	139
fe10f448d641 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 9a8a7f680dd6 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
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	142
9a8a7f680dd6 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
9a8a7f680dd6 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:
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	145
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed 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 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	147
9a8a7f680dd6 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:
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	149
6 39a6e46cdda3 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 9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	159 tools/protein_analysis/promoter2.xml
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	160 tools/protein_analysis/promoter2.py
5 ef7ceca37e3f 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
ef7ceca37e3f 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 39a6e46cdda3 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
39a6e46cdda3 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 9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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
9a8a7f680dd6 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 @ 7:5e62aefb2918 draft