Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/README @ 7:9b45a8743100 draft
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
author | peterjc |
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date | Mon, 30 Jul 2012 10:25:07 -0400 |
parents | a290c6d4e658 |
children | 976a5f2833cd |
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1 This package contains Galaxy wrappers for a selection of standalone command |
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2 line protein analysis tools: |
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3 |
7
9b45a8743100
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4 * SignalP 3.0, THMHMM 2.0, Promoter 2.0 from the Center for Biological |
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5 Sequence Analysis at the Technical University of Denmark, |
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6 http://www.cbs.dtu.dk/cbs/ |
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7 |
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8 * WoLF PSORT v0.2 from http://wolfpsort.org/ |
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9 |
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10 Also, the RXLR motif tool uses SignalP 3.0 and HMMER 2.3.2 internally. |
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11 |
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12 To use these Galaxy wrappers you must first install the command line tools. |
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13 At the time of writing they are all free for academic use. |
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14 |
7
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15 These wrappers are copyright 2010-2012 by Peter Cock, James Hutton Institute |
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16 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
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17 See the included LICENCE file for details (an MIT style open source licence). |
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18 |
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19 Requirements |
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20 ============ |
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21 |
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22 First install those command line tools you wish to use the wrappers for: |
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23 |
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24 1. Install the command line version of SignalP 3.0 and ensure "signalp" is |
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25 on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/ |
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26 |
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27 2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on |
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28 the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/ |
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29 |
7
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Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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30 3. Install the command line version of Promoter 2.0 and ensure "promoter" is |
9b45a8743100
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents:
6
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31 on the PATH, see: http://www.cbs.dtu.dk/services/Promoter |
9b45a8743100
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
parents:
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32 |
9b45a8743100
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
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33 4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary" |
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34 is on the PATH (we use an extra wrapper script to change to the WoLF PSORT |
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35 directory, run runWolfPsortSummary, and then change back to the original |
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36 directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/ |
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37 |
7
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38 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2) |
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39 but put it on the path under the name hmmsearch2 (allowing it to co-exist |
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40 with HMMER 3), or edit rlxr_motif.py accordingly. |
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41 |
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42 Verify each of the tools is installed and working from the command line |
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43 (when logged in as the Galaxy user if appropriate). |
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44 |
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45 Manual Installation |
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46 =================== |
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47 |
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48 1. Create a folder tools/protein_analysis under your Galaxy installation. |
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49 This folder name is not critical, and can be changed if desired - you |
9b45a8743100
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50 must update the paths used in tool_conf.xml to match. |
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51 |
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52 2. Copy/move the following files (from this archive) there: |
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53 |
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54 tmhmm2.xml (Galaxy tool definition) |
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55 tmhmm2.py (Python wrapper script) |
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56 |
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57 signalp3.xml (Galaxy tool definition) |
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58 signalp3.py (Python wrapper script) |
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59 |
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60 promoter2.xml (Galaxy tool definition) |
9b45a8743100
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
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61 promoter2.py (Python wrapper script) |
9b45a8743100
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
peterjc
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62 |
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63 wolf_psort.xml (Galaxy tool definition) |
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64 wolf_psort.py (Python wrapper script) |
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65 |
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66 rxlr_motifs.xml (Galaxy tool definition) |
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67 rxlr_motifs.py (Python script) |
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68 |
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69 seq_analysis_utils.py (shared Python code) |
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70 LICENCE |
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71 README (this file) |
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72 |
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73 3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND |
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74 also tool_conf.xml.sample (to run the tests) to include the new tools |
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75 by adding: |
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76 |
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77 <section name="Protein sequence analysis" id="protein_analysis"> |
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78 <tool file="protein_analysis/tmhmm2.xml" /> |
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79 <tool file="protein_analysis/signalp3.xml" /> |
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80 <tool file="protein_analysis/wolf_psort.xml" /> |
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81 <tool file="protein_analysis/rxlr_motifs.xml" /> |
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82 </section> |
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83 <section name="Nucleotide sequence analysis" id="nucleotide_analysis"> |
9b45a8743100
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84 <tool file="protein_analysis/promoter2.xml" /> |
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85 </section> |
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86 |
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87 Leave out the lines for any tools you do not wish to use in Galaxy. |
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88 |
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89 4. Copy/move the following test files (from these archive) to Galaxy |
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90 subfolder test-data: |
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91 |
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92 four_human_proteins.fasta |
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93 four_human_proteins_signalp3.tabular |
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94 four_human_proteins_tmhmm2.tabular |
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95 empty.fasta |
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96 empty_tmhmm2.tabular |
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97 empty_signalp3.tabular |
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98 |
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99 5. Run the Galaxy functional tests for these new wrappers with: |
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100 |
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101 ./run_functional_tests.sh -id tmhmm2 |
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102 ./run_functional_tests.sh -id signalp3 |
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103 |
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104 Alternatively, this should work (assuming you left the name and id as shown in |
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105 the XML file tool_conf.xml.sample): |
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106 |
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107 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis |
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108 |
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109 6. Restart Galaxy and check the new tools are shown and work. |
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110 |
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111 |
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112 History |
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113 ======= |
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114 |
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115 v0.0.1 - Initial release |
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116 v0.0.2 - Corrected some typos in the help text |
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117 - Renamed test output file to use Galaxy convention of *.tabular |
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118 v0.0.3 - Check for tmhmm2 silent failures (no output) |
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119 - Additional unit tests |
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120 v0.0.4 - Ignore comment lines in tmhmm2 output. |
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121 v0.0.5 - Explicitly request tmhmm short output (may not be the default) |
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122 v0.0.6 - Improvement to how sub-jobs are run (should be faster) |
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123 v0.0.7 - Change SignalP default truncation from 60 to 70 to match the |
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124 SignalP webservice. |
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125 v0.0.8 - Added WoLF PSORT wrapper to the suite. |
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126 v0.0.9 - Added our RXLR motifs tool to the suite. |
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127 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) |
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128 - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter |
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129 |
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130 Developers |
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131 ========== |
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132 |
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133 This script and other tools are being developed on the following hg branch: |
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134 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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135 |
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136 This incorporates the previously used hg branch: |
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137 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis |
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138 |
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139 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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140 the following command from the Galaxy root folder: |
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141 |
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142 tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular |
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143 |
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144 Check this worked: |
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145 |
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146 $ tar -tzf tmhmm_signalp_etc.tar.gz |
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147 tools/protein_analysis/LICENSE |
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148 tools/protein_analysis/README |
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149 tools/protein_analysis/suite_config.xml |
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150 tools/protein_analysis/seq_analysis_utils.py |
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151 tools/protein_analysis/signalp3.xml |
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152 tools/protein_analysis/signalp3.py |
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153 tools/protein_analysis/tmhmm2.xml |
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154 tools/protein_analysis/tmhmm2.py |
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155 tools/protein_analysis/promoter2.xml |
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156 tools/protein_analysis/promoter2.py |
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157 tools/protein_analysis/wolf_psort.xml |
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158 tools/protein_analysis/wolf_psort.py |
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159 tools/protein_analysis/rxlr_motifs.xml |
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160 tools/protein_analysis/rxrl_motifs.py |
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161 test-data/four_human_proteins.fasta |
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162 test-data/four_human_proteins.signalp3.tabular |
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163 test-data/four_human_proteins.tmhmm2.tabular |
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164 test-data/empty.fasta |
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165 test-data/empty_tmhmm2.tabular |
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166 test-data/empty_signalp3.tabular |