Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README.rst @ 26:20139cb4c844 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
author peterjc
date Wed, 13 May 2015 06:14:42 -0400
parents 41a42022f815
children 9e36a1b9302d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
1 This package contains Galaxy wrappers for a selection of standalone command
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
2 line protein analysis tools:
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
3
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
5 Sequence Analysis at the Technical University of Denmark,
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
6 http://www.cbs.dtu.dk/cbs/
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
7
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
8 * WoLF PSORT v0.2 from http://wolfpsort.org/
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
9
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
10 * PSORTb v3 from http://www.psort.org/downloads/index.html
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
11
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
13
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
14 To use these Galaxy wrappers you must first install the command line tools.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
15 At the time of writing they are all free for academic use, or open source.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
16
26
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
17 These wrappers are copyright 2010-2015 by Peter Cock, James Hutton Institute
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
20 See the included LICENCE file for details (MIT open source licence).
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
21
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
22 The wrappers are available from the Galaxy Tool Shed
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
23 http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
25 Citation
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
26 ========
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
27
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
28 If you use any of these Galaxy tools in work leading to a scientific
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
29 publication, in addition to citing the invididual underlying tools, please cite:
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
30
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
31 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
32 Galaxy tools and workflows for sequence analysis with applications
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
33 in molecular plant pathology. PeerJ 1:e167
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
34 http://dx.doi.org/10.7717/peerj.167
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
35
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
36 Full reference information is included in the help text for each tool.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
37
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
38
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
39 Requirements
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
40 ============
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
41
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
42 First install those command line tools you wish to use the wrappers for:
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
43
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
44 1. Install the command line version of SignalP 3.0 and ensure ``signalp`` is
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
45 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
46
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
47 2. Install the command line version of TMHMM 2.0 and ensure ``tmhmm`` is on
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
48 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
49
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
50 3. Install the command line version of Promoter 2.0 and ensure ``promoter`` is
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
51 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
52
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
53 4. Install the WoLF PSORT v0.2 package, and ensure ``runWolfPsortSummary``
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
54 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
55 directory, run runWolfPsortSummary, and then change back to the original
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
56 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
57
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
58 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
59 but put it on the path under the name ``hmmsearch2`` (allowing it to
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
60 co-exist with HMMER 3), or edit ``rlxr_motif.py`` accordingly.
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
61
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
62 Verify each of the tools is installed and working from the command line
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
63 (when logged in as the Galaxy user if appropriate).
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
64
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
65
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
66 Manual Installation
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
67 ===================
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
68
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
69 1. Create a folder ``tools/protein_analysis`` under your Galaxy installation.
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
70 This folder name is not critical, and can be changed if desired - you
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
71 must update the paths used in ``tool_conf.xml`` to match.
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
72
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
73 2. Copy/move the following files (from this archive) there:
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
74
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
75 * ``tmhmm2.xml`` (Galaxy tool definition)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
76 * ``tmhmm2.py`` (Python wrapper script)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
77
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
78 * ``signalp3.xml`` (Galaxy tool definition)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
79 * ``signalp3.py`` (Python wrapper script)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
80
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
81 * ``promoter2.xml`` (Galaxy tool definition)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
82 * ``promoter2.py`` (Python wrapper script)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
83
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
84 * ``psortb.xml`` (Galaxy tool definition)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
85 * ``psortb.py`` (Python wrapper script)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
86
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
87 * ``wolf_psort.xml`` (Galaxy tool definition)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
88 * ``wolf_psort.py`` (Python wrapper script)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
89
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
90 * ``rxlr_motifs.xml`` (Galaxy tool definition)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
91 * ``rxlr_motifs.py`` (Python script)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
92
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
93 * ``seq_analysis_utils.py`` (shared Python code)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
94 * ``LICENCE``
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
95 * ``README.rst`` (this file)
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
96
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
97 3. Edit your Galaxy conjuration file ``tool_conf.xml`` to include the
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
98 new tools by adding::
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
99
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
100 <section name="Protein sequence analysis" id="protein_analysis">
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
101 <tool file="protein_analysis/tmhmm2.xml" />
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
102 <tool file="protein_analysis/signalp3.xml" />
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
103 <tool file="protein_analysis/psortb.xml" />
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
104 <tool file="protein_analysis/wolf_psort.xml" />
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
105 <tool file="protein_analysis/rxlr_motifs.xml" />
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
106 </section>
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
107 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
108 <tool file="protein_analysis/promoter2.xml" />
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
109 </section>
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
110
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
111 Leave out the lines for any tools you do not wish to use in Galaxy.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
112
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
113 4. Copy/move the ``test-data/*`` files (from this archive) to Galaxy's
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
114 subfolder ``test-data/``.
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
115
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
116 5. Run the Galaxy functional tests for these new wrappers with::
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
117
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
118 $ ./run_tests.sh -id tmhmm2
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
119 $ ./run_tests.sh -id signalp3
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
120 $ ./run_tests.sh -id Psortb
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
121 $ ./run_tests.sh -id rxlr_motifs
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
122
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
123 Alternatively, this should work (assuming you left the seciont name and id
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
124 as shown above in your XML file ``tool_conf.xml``)::
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
125
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
126 $ ./run_tests.sh -sid Protein_sequence_analysis-protein_analysis
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
127
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
128 To check the section ID expected, use:
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
129
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
130 $ ./run_tests.sh -list
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
131
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
132 6. Restart Galaxy and check the new tools are shown and work.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
133
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
134
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
135 History
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
136 =======
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
137
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
138 ======= ======================================================================
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
139 Version Changes
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
140 ------- ----------------------------------------------------------------------
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
141 v0.0.1 - Initial release
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
142 v0.0.2 - Corrected some typos in the help text
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
143 - Renamed test output file to use Galaxy convention of ``*.tabular``
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
144 v0.0.3 - Check for tmhmm2 silent failures (no output)
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
145 - Additional unit tests
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
146 v0.0.4 - Ignore comment lines in tmhmm2 output.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
147 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
148 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
149 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
150 SignalP webservice.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
151 v0.0.8 - Added WoLF PSORT wrapper to the suite.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
152 v0.0.9 - Added our RXLR motifs tool to the suite.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
153 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
154 - Support Galaxy's ``<parallelism>`` tag for SignalP, TMHMM & Promoter
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
155 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
156 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
157 - Use SGE style ``$NSLOTS`` for thread count (otherwise default to 4)
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
158 v0.1.3 - Added missing file ``whisson_et_al_rxlr_eer_cropped.hmm`` to Tool Shed
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
159 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
160 contributed by Konrad Paszkiewicz.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
161 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
162 files accidentally included previously via a wildcard).
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
163 v0.2.2 - Include missing test files.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
164 v0.2.3 - Added unit tests for WoLF PSORT.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
165 v0.2.4 - Added unit tests for Promoter 2
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
166 v0.2.5 - Link to Tool Shed added to help text and this documentation.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
167 - More unit tests.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
168 - Fixed bug with RXLR tool and empty FASTA files.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
169 - Fixed typo in the RXLR tool help text.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
170 - Updated citation information (Cock et al. 2013).
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
171 - Adopted standard MIT licence.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
172 - Use reStructuredText for this README file.
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
175 - Updated the ``suite_config.xml`` file (overdue).
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
176 - Tool definition now embeds citation information.
26
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
177 v0.2.7 - Style cleanup in Python scripts.
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
178 v0.2.8 - Reorder XML elements (internal change only).
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
179 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
180 ======= ======================================================================
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
181
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
182
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
183 Developers
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
184 ==========
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
185
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 24
diff changeset
186 This script and other tools were initially developed on the following hg branches:
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
187 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
188 http://bitbucket.org/peterjc/galaxy-central/src/tools
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
189
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
190 Development has now moved to a dedicated GitHub repository:
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
191 https://github.com/peterjc/pico_galaxy/tree/master/tools
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
192
26
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
193
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
194 For pushing a release to the test or main "Galaxy Tool Shed", use the following
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
195 Planemo commands (which requires you have set your Tool Shed access details in
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
196 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
197
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
198 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
199 ...
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
200
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
201 or::
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
202
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
203 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
204 ...
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
205
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
206 To just build and check the tar ball, use::
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
207
26
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
208 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/protein_analysis/
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
209 ...
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
210 $ tar -tzf shed_upload.tar.gz
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
211 test-data/Adenovirus.fasta
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
212 test-data/Adenovirus.promoter2.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
213 test-data/empty.fasta
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
214 test-data/empty_promoter2.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
215 test-data/empty_psortb_terse.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
216 test-data/empty_rxlr.Bhattacharjee2006.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
217 test-data/empty_rxlr.Whisson2007.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
218 test-data/empty_rxlr.Win2007.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
219 test-data/empty_signalp3.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
220 test-data/empty_tmhmm2.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
221 test-data/empty_wolf_psort.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
222 test-data/four_human_proteins.fasta
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
223 test-data/four_human_proteins.signalp3.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
224 test-data/four_human_proteins.tmhmm2.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
225 test-data/four_human_proteins.wolf_psort.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
226 test-data/k12_ten_proteins.fasta
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
227 test-data/k12_ten_proteins_psortb_p_terse.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
228 test-data/rxlr_win_et_al_2007.fasta
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
229 test-data/rxlr_win_et_al_2007.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
230 test-data/rxlr_win_et_al_2007_sp3.tabular
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
231 tools/protein_analysis/LICENSE.txt
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
232 tools/protein_analysis/README.rst
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
233 tools/protein_analysis/promoter2.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
234 tools/protein_analysis/promoter2.xml
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
235 tools/protein_analysis/psortb.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
236 tools/protein_analysis/psortb.xml
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
237 tools/protein_analysis/rxlr_motifs.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
238 tools/protein_analysis/rxlr_motifs.xml
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
239 tools/protein_analysis/seq_analysis_utils.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
240 tools/protein_analysis/signalp3.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
241 tools/protein_analysis/signalp3.xml
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
242 tools/protein_analysis/suite_config.xml
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
243 tools/protein_analysis/tmhmm2.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
244 tools/protein_analysis/tmhmm2.xml
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
245 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
246 tools/protein_analysis/wolf_psort.py
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
peterjc
parents: 25
diff changeset
247 tools/protein_analysis/wolf_psort.xml
24
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
248
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
249 This simplifies ensuring a consistent set of files is bundled each time,
ee10017fcd80 Uploaded v0.2.5 preview 8, omitted README.rst in last upload
peterjc
parents:
diff changeset
250 including all the relevant test files.