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comparison tools/protein_analysis/README.rst @ 17:e6cc27d182a8 draft

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Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
author peterjc
date Fri, 21 Nov 2014 08:19:09 -0500
parents 7de64c8b258d
children eb6ac44d4b8e
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39 Requirements 39 Requirements
40 ============ 40 ============
41 41
42 First install those command line tools you wish to use the wrappers for: 42 First install those command line tools you wish to use the wrappers for:
43 43
44 1. Install the command line version of SignalP 3.0 and ensure "signalp" is 44 1. Install the command line version of SignalP 3.0 and ensure ``signalp`` is
45 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/ 45 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
46 46
47 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on 47 2. Install the command line version of TMHMM 2.0 and ensure ``tmhmm`` is on
48 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/ 48 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
49 49
50 3. Install the command line version of Promoter 2.0 and ensure "promoter" is 50 3. Install the command line version of Promoter 2.0 and ensure ``promoter`` is
51 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter 51 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
52 52
53 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary" 53 4. Install the WoLF PSORT v0.2 package, and ensure ``runWolfPsortSummary``
54 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT 54 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
55 directory, run runWolfPsortSummary, and then change back to the original 55 directory, run runWolfPsortSummary, and then change back to the original
56 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/ 56 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
57 57
58 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2) 58 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
59 but put it on the path under the name hmmsearch2 (allowing it to co-exist 59 but put it on the path under the name ``hmmsearch2`` (allowing it to
60 with HMMER 3), or edit rlxr_motif.py accordingly. 60 co-exist with HMMER 3), or edit ``rlxr_motif.py`` accordingly.
61 61
62 Verify each of the tools is installed and working from the command line 62 Verify each of the tools is installed and working from the command line
63 (when logged in as the Galaxy user if appropriate). 63 (when logged in as the Galaxy user if appropriate).
64 64
65 65
66 Manual Installation 66 Manual Installation
67 =================== 67 ===================
68 68
69 1. Create a folder tools/protein_analysis under your Galaxy installation. 69 1. Create a folder ``tools/protein_analysis`` under your Galaxy installation.
70 This folder name is not critical, and can be changed if desired - you 70 This folder name is not critical, and can be changed if desired - you
71 must update the paths used in tool_conf.xml to match. 71 must update the paths used in ``tool_conf.xml`` to match.
72 72
73 2. Copy/move the following files (from this archive) there: 73 2. Copy/move the following files (from this archive) there:
74 74
75 * tmhmm2.xml (Galaxy tool definition) 75 * ``tmhmm2.xml`` (Galaxy tool definition)
76 * tmhmm2.py (Python wrapper script) 76 * ``tmhmm2.py`` (Python wrapper script)
77 77
78 * signalp3.xml (Galaxy tool definition) 78 * ``signalp3.xml`` (Galaxy tool definition)
79 * signalp3.py (Python wrapper script) 79 * ``signalp3.py`` (Python wrapper script)
80 80
81 * promoter2.xml (Galaxy tool definition) 81 * ``promoter2.xml`` (Galaxy tool definition)
82 * promoter2.py (Python wrapper script) 82 * ``promoter2.py`` (Python wrapper script)
83 83
84 * psortb.xml (Galaxy tool definition) 84 * ``psortb.xml`` (Galaxy tool definition)
85 * psortb.py (Python wrapper script) 85 * ``psortb.py`` (Python wrapper script)
86 86
87 * wolf_psort.xml (Galaxy tool definition) 87 * ``wolf_psort.xml`` (Galaxy tool definition)
88 * wolf_psort.py (Python wrapper script) 88 * ``wolf_psort.py`` (Python wrapper script)
89 89
90 * rxlr_motifs.xml (Galaxy tool definition) 90 * ``rxlr_motifs.xml`` (Galaxy tool definition)
91 * rxlr_motifs.py (Python script) 91 * ``rxlr_motifs.py`` (Python script)
92 92
93 * seq_analysis_utils.py (shared Python code) 93 * ``seq_analysis_utils.py`` (shared Python code)
94 * LICENCE 94 * ``LICENCE``
95 * README.rst (this file) 95 * ``README.rst`` (this file)
96 96
97 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND 97 3. Edit your Galaxy conjuration file ``tool_conf.xml`` to include the
98 also tool_conf.xml.sample (to run the tests) to include the new tools 98 new tools by adding::
99 by adding::
100 99
101 <section name="Protein sequence analysis" id="protein_analysis"> 100 <section name="Protein sequence analysis" id="protein_analysis">
102 <tool file="protein_analysis/tmhmm2.xml" /> 101 <tool file="protein_analysis/tmhmm2.xml" />
103 <tool file="protein_analysis/signalp3.xml" /> 102 <tool file="protein_analysis/signalp3.xml" />
104 <tool file="protein_analysis/psortb.xml" /> 103 <tool file="protein_analysis/psortb.xml" />
109 <tool file="protein_analysis/promoter2.xml" /> 108 <tool file="protein_analysis/promoter2.xml" />
110 </section> 109 </section>
111 110
112 Leave out the lines for any tools you do not wish to use in Galaxy. 111 Leave out the lines for any tools you do not wish to use in Galaxy.
113 112
114 4. Copy/move the test-data files (from this archive) to Galaxy's 113 4. Copy/move the ``test-data/*`` files (from this archive) to Galaxy's
115 subfolder test-data. 114 subfolder ``test-data/``.
116 115
117 5. Run the Galaxy functional tests for these new wrappers with:: 116 5. Run the Galaxy functional tests for these new wrappers with::
118 117
119 ./run_functional_tests.sh -id tmhmm2 118 $ ./run_tests.sh -id tmhmm2
120 ./run_functional_tests.sh -id signalp3 119 $ ./run_tests.sh -id signalp3
121 ./run_functional_tests.sh -id Psortb 120 $ ./run_tests.sh -id Psortb
122 ./run_functional_tests.sh -id rxlr_motifs 121 $ ./run_tests.sh -id rxlr_motifs
123 122
124 Alternatively, this should work (assuming you left the name and id as shown in 123 Alternatively, this should work (assuming you left the seciont name and id
125 the XML file tool_conf.xml.sample):: 124 as shown above in your XML file ``tool_conf.xml``)::
126 125
127 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis 126 $ ./run_tests.sh -sid Protein_sequence_analysis-protein_analysis
128 127
129 To check the section ID expected, use ./run_functional_tests.sh -list 128 To check the section ID expected, use:
129
130 $ ./run_tests.sh -list
130 131
131 6. Restart Galaxy and check the new tools are shown and work. 132 6. Restart Galaxy and check the new tools are shown and work.
132 133
133 134
134 History 135 History
137 ======= ====================================================================== 138 ======= ======================================================================
138 Version Changes 139 Version Changes
139 ------- ---------------------------------------------------------------------- 140 ------- ----------------------------------------------------------------------
140 v0.0.1 - Initial release 141 v0.0.1 - Initial release
141 v0.0.2 - Corrected some typos in the help text 142 v0.0.2 - Corrected some typos in the help text
142 - Renamed test output file to use Galaxy convention of *.tabular 143 - Renamed test output file to use Galaxy convention of ``*.tabular``
143 v0.0.3 - Check for tmhmm2 silent failures (no output) 144 v0.0.3 - Check for tmhmm2 silent failures (no output)
144 - Additional unit tests 145 - Additional unit tests
145 v0.0.4 - Ignore comment lines in tmhmm2 output. 146 v0.0.4 - Ignore comment lines in tmhmm2 output.
146 v0.0.5 - Explicitly request tmhmm short output (may not be the default) 147 v0.0.5 - Explicitly request tmhmm short output (may not be the default)
147 v0.0.6 - Improvement to how sub-jobs are run (should be faster) 148 v0.0.6 - Improvement to how sub-jobs are run (should be faster)
148 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the 149 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the
149 SignalP webservice. 150 SignalP webservice.
150 v0.0.8 - Added WoLF PSORT wrapper to the suite. 151 v0.0.8 - Added WoLF PSORT wrapper to the suite.
151 v0.0.9 - Added our RXLR motifs tool to the suite. 152 v0.0.9 - Added our RXLR motifs tool to the suite.
152 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) 153 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
153 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter 154 - Support Galaxy's ``<parallelism>`` tag for SignalP, TMHMM & Promoter
154 v0.1.1 - Fixed an error in the header of the tabular output from Promoter 155 v0.1.1 - Fixed an error in the header of the tabular output from Promoter
155 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors 156 v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors
156 - Use SGE style $NSLOTS for thread count (otherwise default to 4) 157 - Use SGE style ``$NSLOTS`` for thread count (otherwise default to 4)
157 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed 158 v0.1.3 - Added missing file ``whisson_et_al_rxlr_eer_cropped.hmm`` to Tool Shed
158 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work 159 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
159 contributed by Konrad Paszkiewicz. 160 contributed by Konrad Paszkiewicz.
160 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray 161 v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
161 files accidentally included previously via a wildcard). 162 files accidentally included previously via a wildcard).
162 v0.2.2 - Include missing test files. 163 v0.2.2 - Include missing test files.
168 - Fixed typo in the RXLR tool help text. 169 - Fixed typo in the RXLR tool help text.
169 - Updated citation information (Cock et al. 2013). 170 - Updated citation information (Cock et al. 2013).
170 - Adopted standard MIT licence. 171 - Adopted standard MIT licence.
171 - Use reStructuredText for this README file. 172 - Use reStructuredText for this README file.
172 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 173 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
174 v0.2.6 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
175 - Updated the ``suite_config.xml`` file (overdue).
176 - Tool definition now embeds citation information.
173 ======= ====================================================================== 177 ======= ======================================================================
174 178
175 179
176 Developers 180 Developers
177 ========== 181 ==========
178 182
179 This script and other tools are being developed on the following hg branches: 183 This script and other tools were initially developed on the following hg branches:
180 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis 184 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
181 http://bitbucket.org/peterjc/galaxy-central/src/tools 185 http://bitbucket.org/peterjc/galaxy-central/src/tools
182 186
183 Development has now moved to a dedicated GitHub repository: 187 Development has now moved to a dedicated GitHub repository:
184 https://github.com/peterjc/pico_galaxy/tree/master/tools 188 https://github.com/peterjc/pico_galaxy/tree/master/tools