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annotate tools/protein_analysis/README @ 0:a2eeeaa6f75e

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Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:37:26 -0400
parents
children 9a8a7f680dd6
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a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 This package contains Galaxy wrappers for two standalone command line protein
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2 analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological
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3 Sequence Analysis at the Technical University of Denmark,
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4 http://www.cbs.dtu.dk/cbs/
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5
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6 To use these Galaxy wrappers you must first install the CBS command line
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7 tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for
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8 academic use.
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9
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10 These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights
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11 reserved. See the included LICENCE file for details.
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12
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13 Installation
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14 ============
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15
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16 1. Install the command line version of SignalP 3.0 and ensure it is on the
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17 PATH, see: http://www.cbs.dtu.dk/services/SignalP/
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18
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19 2. Install the command line version of TMHMM 2.0 and ensure it is on the
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20 PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
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21
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22 3. Create a folder tools/protein_analysis under your Galaxy installation.
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24 4. Copy/move the following files (from this archive) there:
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26 tmhmm2.xml (Galaxy tool definition)
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27 tmhmm2.py (Python wrapper script)
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28 signalp3.xml (Galaxy tool definition)
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29 signalp3.py (Python wrapper script)
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30 seq_analysis_utils.py (shared Python code)
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31 README (optional)
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32
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33 5. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
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34 also tool_conf.xml.sample (to run the tests) to include the two new tools
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35 by adding:
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37 <section name="Protein sequence analysis" id="protein_analysis">
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38 <tool file="protein_analysis/tmhmm2.xml" />
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39 <tool file="protein_analysis/signalp3.xml" />
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40 </section>
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41
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42 6. Copy/move the following test files (from these archive) to Galaxy
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43 subfolder test-data:
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44
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45 four_human_proteins.fasta
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46 four_human_proteins.signalp3.tsv
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47 four_human_proteins.tmhmm2.tsv
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48
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49 7. Run the Galaxy functional tests for these new wrappers with:
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50
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51 ./run_functional_tests.sh -id tmhmm2
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52 ./run_functional_tests.sh -id signalp3
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53
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54 Alternatively, this should work (assuming you left the name and id as shown in
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55 the XML file tool_conf.xml.sample):
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56
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57 ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
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58
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59 8. Restart Galaxy and check the new tools are shown and work.