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1 Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
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2 of mgf files and performs X! Tandem and OMSSA searches on these via
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3 SearchGUI and merges the results using PeptideShaker.
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4
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5 For Galaxy-P we are installing this tool via CloudBioLinux
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6 (https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
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7 this fabric script may not be exactly appropriate for your environment
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8 it may serve as a template for how to install this software. In
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9 particular these tools require CLI wrappers to be placed for
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10 PeptideShaker and SearchGUI that can be installed as demostrated in
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11 these fabric functions.
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12
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13 Note: Also SearchGUI requires a version greater than 1.12.2 which
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14 contained several bugs preventing this from working on the
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15 command-line and via Linux.
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16
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17 Also, PeptideShaker may require xvfb to simulate an X environment if
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18 this is installed on a headless server.
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19 # Obtaining Tools
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20
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21 Repositories for all Galaxy-P tools can be found at
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22 https:/bitbucket.org/galaxyp/.
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23
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24 # Contact
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25
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26 Please send suggestions for improvements and bug reports to
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27 jmchilton@gmail.com.
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28
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29 # License
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30
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31 All Galaxy-P tools are licensed under the Apache License Version 2.0
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32 unless otherwise documented.
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33
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34 # Tool Versioning
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35
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36 Galaxy-P tools will have versions of the form X.Y.Z. Versions
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37 differing only after the second decimal should be completely
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38 compatible with each other. Breaking changes should result in an
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39 increment of the number before and/or after the first decimal. All
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40 tools of version less than 1.0.0 should be considered beta.
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