Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/README.rst @ 23:e1996f0f4e85 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"v0.2.13 - Python 3 fix for raising StopIteration"
author peterjc
date Thu, 17 Jun 2021 17:59:33 +0000
parents e1afa4b0b682
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
1 This package contains Galaxy wrappers for a selection of standalone command
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
2 line protein analysis tools:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
3
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
5 Sequence Analysis at the Technical University of Denmark,
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
6 http://www.cbs.dtu.dk/cbs/
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
7
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
8 * WoLF PSORT v0.2 from http://wolfpsort.org/
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
9
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
10 * PSORTb v3 from http://www.psort.org/downloads/index.html
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
11
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
12 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
13
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
14 To use these Galaxy wrappers you must first install the command line tools.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
15 At the time of writing they are all free for academic use, or open source.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
16
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
17 These wrappers are copyright 2010-2015 by Peter Cock, James Hutton Institute
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
18 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
19 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
20 See the included LICENCE file for details (MIT open source licence).
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
21
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
22 The wrappers are available from the Galaxy Tool Shed
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
23 http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
24
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
25 Citation
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
26 ========
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
27
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
28 If you use any of these Galaxy tools in work leading to a scientific
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
29 publication, in addition to citing the invididual underlying tools, please cite:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
30
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
31 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
32 Galaxy tools and workflows for sequence analysis with applications
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
33 in molecular plant pathology. PeerJ 1:e167
21
238eae32483c "Check this is up to date with all 2020 changes (black etc)"
peterjc
parents: 20
diff changeset
34 https://doi.org/10.7717/peerj.167
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
35
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
36 Full reference information is included in the help text for each tool.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
37
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
38
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
39 Requirements
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
40 ============
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
41
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
42 First install those command line tools you wish to use the wrappers for:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
43
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
44 1. Install the command line version of SignalP 3.0 and ensure ``signalp`` is
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
45 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
46
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
47 2. Install the command line version of TMHMM 2.0 and ensure ``tmhmm`` is on
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
48 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
49
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
50 3. Install the command line version of Promoter 2.0 and ensure ``promoter`` is
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
51 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
52
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
53 4. Install the WoLF PSORT v0.2 package, and ensure ``runWolfPsortSummary``
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
54 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
55 directory, run runWolfPsortSummary, and then change back to the original
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
56 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
57
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
58 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
59 but put it on the path under the name ``hmmsearch2`` (allowing it to
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
60 co-exist with HMMER 3), or edit ``rlxr_motif.py`` accordingly.
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
61
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
62 Verify each of the tools is installed and working from the command line
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
63 (when logged in as the Galaxy user if appropriate).
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
64
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
65
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
66 Manual Installation
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
67 ===================
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
68
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
69 1. Create a folder ``tools/protein_analysis`` under your Galaxy installation.
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
70 This folder name is not critical, and can be changed if desired - you
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
71 must update the paths used in ``tool_conf.xml`` to match.
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
72
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
73 2. Copy/move the following files (from this archive) there:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
74
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
75 * ``tmhmm2.xml`` (Galaxy tool definition)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
76 * ``tmhmm2.py`` (Python wrapper script)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
77
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
78 * ``signalp3.xml`` (Galaxy tool definition)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
79 * ``signalp3.py`` (Python wrapper script)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
80
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
81 * ``promoter2.xml`` (Galaxy tool definition)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
82 * ``promoter2.py`` (Python wrapper script)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
83
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
84 * ``psortb.xml`` (Galaxy tool definition)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
85 * ``psortb.py`` (Python wrapper script)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
86
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
87 * ``wolf_psort.xml`` (Galaxy tool definition)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
88 * ``wolf_psort.py`` (Python wrapper script)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
89
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
90 * ``rxlr_motifs.xml`` (Galaxy tool definition)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
91 * ``rxlr_motifs.py`` (Python script)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
92
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
93 * ``seq_analysis_utils.py`` (shared Python code)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
94 * ``LICENCE``
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
95 * ``README.rst`` (this file)
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
96
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
97 3. Edit your Galaxy conjuration file ``tool_conf.xml`` to include the
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
98 new tools by adding::
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
99
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
100 <section name="Protein sequence analysis" id="protein_analysis">
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
101 <tool file="protein_analysis/tmhmm2.xml" />
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
102 <tool file="protein_analysis/signalp3.xml" />
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
103 <tool file="protein_analysis/psortb.xml" />
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
104 <tool file="protein_analysis/wolf_psort.xml" />
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
105 <tool file="protein_analysis/rxlr_motifs.xml" />
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
106 </section>
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
107 <section name="Nucleotide sequence analysis" id="nucleotide_analysis">
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
108 <tool file="protein_analysis/promoter2.xml" />
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
109 </section>
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
110
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
111 Leave out the lines for any tools you do not wish to use in Galaxy.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
112
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
113 4. Copy/move the ``test-data/*`` files (from this archive) to Galaxy's
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
114 subfolder ``test-data/``.
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
115
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
116 5. Run the Galaxy functional tests for these new wrappers with::
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
117
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
118 $ ./run_tests.sh -id tmhmm2
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
119 $ ./run_tests.sh -id signalp3
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
120 $ ./run_tests.sh -id Psortb
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
121 $ ./run_tests.sh -id rxlr_motifs
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
122
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
123 Alternatively, this should work (assuming you left the seciont name and id
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
124 as shown above in your XML file ``tool_conf.xml``)::
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
125
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
126 $ ./run_tests.sh -sid Protein_sequence_analysis-protein_analysis
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
127
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
128 To check the section ID expected, use:
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
129
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
130 $ ./run_tests.sh -list
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
131
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
132 6. Restart Galaxy and check the new tools are shown and work.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
133
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
134
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
135 History
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
136 =======
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
137
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
138 ======= ======================================================================
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
139 Version Changes
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
140 ------- ----------------------------------------------------------------------
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
141 v0.0.1 - Initial release
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
142 v0.0.2 - Corrected some typos in the help text
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
143 - Renamed test output file to use Galaxy convention of ``*.tabular``
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
144 v0.0.3 - Check for tmhmm2 silent failures (no output)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
145 - Additional unit tests
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
146 v0.0.4 - Ignore comment lines in tmhmm2 output.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
147 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
148 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
149 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
150 SignalP webservice.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
151 v0.0.8 - Added WoLF PSORT wrapper to the suite.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
152 v0.0.9 - Added our RXLR motifs tool to the suite.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
153 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
154 - Support Galaxy's ``<parallelism>`` tag for SignalP, TMHMM & Promoter
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
155 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
156 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
157 - Use SGE style ``$NSLOTS`` for thread count (otherwise default to 4)
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
158 v0.1.3 - Added missing file ``whisson_et_al_rxlr_eer_cropped.hmm`` to Tool Shed
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
159 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
160 contributed by Konrad Paszkiewicz.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
161 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
162 files accidentally included previously via a wildcard).
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
163 v0.2.2 - Include missing test files.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
164 v0.2.3 - Added unit tests for WoLF PSORT.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
165 v0.2.4 - Added unit tests for Promoter 2
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
166 v0.2.5 - Link to Tool Shed added to help text and this documentation.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
167 - More unit tests.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
168 - Fixed bug with RXLR tool and empty FASTA files.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
169 - Fixed typo in the RXLR tool help text.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
170 - Updated citation information (Cock et al. 2013).
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
171 - Adopted standard MIT licence.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
172 - Use reStructuredText for this README file.
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
175 - Updated the ``suite_config.xml`` file (overdue).
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
176 - Tool definition now embeds citation information.
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
177 v0.2.7 - Style cleanup in Python scripts using ``pep8``.
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
178 v0.2.8 - Reorder XML elements (internal change only).
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
179 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
180 - Record version of Promoter 2 via ``<version_command>``.
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
181 v0.2.9 - Further style cleanup in Python scripts (internal change only).
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
182 v0.2.10 - Style cleanup in Python scripts using ``flake8``.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
183 - Record TMHMM and SignalP wrapper version via ``<version_command>``.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
184 - Python 3 compatible print function and exception handling.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
185 - Python 3 compatible subprocess calling.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
186 - Removed obsolete ``suite_config.xml`` file.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
187 v0.2.11 - Updated RXLR tool dependencies to get HMMER2 via BioConda.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
188 - Use ``<command detect_errors="aggressive">`` (internal change only).
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
189 - Single quote command line arguments (internal change only).
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
190 - Record WoLF PSORT wrapper version via ``<version_command>``.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
191 - Fix error handling in SignalP wrapper.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
192 - Record SignalP version via ``<version_command>``.
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
193 - Internal job splitter will skip starting any pending jobs after a
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
194 child job fails (so the entire task will error out more quickly).
21
238eae32483c "Check this is up to date with all 2020 changes (black etc)"
peterjc
parents: 20
diff changeset
195 v0.2.12 - Fix reporting of HMMER error in RXLR tool.
238eae32483c "Check this is up to date with all 2020 changes (black etc)"
peterjc
parents: 20
diff changeset
196 - Quote command line arguments when RXLR tool calls SignalP.
238eae32483c "Check this is up to date with all 2020 changes (black etc)"
peterjc
parents: 20
diff changeset
197 - Reduce number of temp files if SignalP is run with one thread.
22
e1afa4b0b682 "This is v0.2.12 with black formating and Python 3 next fix etc"
peterjc
parents: 21
diff changeset
198 - Applied black style to the Python code
e1afa4b0b682 "This is v0.2.12 with black formating and Python 3 next fix etc"
peterjc
parents: 21
diff changeset
199 - Python 3 fixes with next function vs method.
23
e1996f0f4e85 "v0.2.13 - Python 3 fix for raising StopIteration"
peterjc
parents: 22
diff changeset
200 v0.2.13 - Python 3 fix for raising StopIteration.
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
201 ======= ======================================================================
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
202
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
203
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
204 Developers
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
205 ==========
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
206
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 16
diff changeset
207 This script and other tools were initially developed on the following hg branches:
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
208 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
209 http://bitbucket.org/peterjc/galaxy-central/src/tools
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
210
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
211 Development has now moved to a dedicated GitHub repository:
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
212 https://github.com/peterjc/pico_galaxy/tree/master/tools
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
213
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
214
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
215 For pushing a release to the test or main "Galaxy Tool Shed", use the following
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
216 Planemo commands (which requires you have set your Tool Shed access details in
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
217 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
218
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
219 $ planemo shed_update -t testtoolshed --check_diff tools/protein_analysis/
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
220 ...
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
221
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
222 or::
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
223
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
224 $ planemo shed_update -t toolshed --check_diff tools/protein_analysis/
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
225 ...
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
226
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
227 To just build and check the tar ball, use::
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
228
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
229 $ planemo shed_upload --tar_only tools/protein_analysis/
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
230 ...
20
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
peterjc
parents: 19
diff changeset
231 $ tar -tzf shed_upload.tar.gz
18
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
232 test-data/Adenovirus.fasta
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
233 test-data/Adenovirus.promoter2.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
234 test-data/empty.fasta
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
235 test-data/empty_promoter2.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
236 test-data/empty_psortb_terse.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
237 test-data/empty_rxlr.Bhattacharjee2006.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
238 test-data/empty_rxlr.Whisson2007.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
239 test-data/empty_rxlr.Win2007.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
240 test-data/empty_signalp3.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
241 test-data/empty_tmhmm2.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
242 test-data/empty_wolf_psort.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
243 test-data/four_human_proteins.fasta
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
244 test-data/four_human_proteins.signalp3.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
245 test-data/four_human_proteins.tmhmm2.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
246 test-data/four_human_proteins.wolf_psort.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
247 test-data/k12_ten_proteins.fasta
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
248 test-data/k12_ten_proteins_psortb_p_terse.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
249 test-data/rxlr_win_et_al_2007.fasta
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
250 test-data/rxlr_win_et_al_2007.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
251 test-data/rxlr_win_et_al_2007_sp3.tabular
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
252 tools/protein_analysis/LICENSE.txt
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
253 tools/protein_analysis/README.rst
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
254 tools/protein_analysis/promoter2.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
255 tools/protein_analysis/promoter2.xml
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
256 tools/protein_analysis/psortb.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
257 tools/protein_analysis/psortb.xml
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
258 tools/protein_analysis/rxlr_motifs.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
259 tools/protein_analysis/rxlr_motifs.xml
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
260 tools/protein_analysis/seq_analysis_utils.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
261 tools/protein_analysis/signalp3.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
262 tools/protein_analysis/signalp3.xml
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
263 tools/protein_analysis/suite_config.xml
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
264 tools/protein_analysis/tmhmm2.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
265 tools/protein_analysis/tmhmm2.xml
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
266 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
267 tools/protein_analysis/wolf_psort.py
eb6ac44d4b8e Suite v0.2.8, record Promoter 2 verion + misc internal updates
peterjc
parents: 17
diff changeset
268 tools/protein_analysis/wolf_psort.xml
16
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
269
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
270 This simplifies ensuring a consistent set of files is bundled each time,
7de64c8b258d Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
peterjc
parents:
diff changeset
271 including all the relevant test files.