Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/README.rst @ 17:e6cc27d182a8 draft
Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
author | peterjc |
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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 |