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1 # msconvert
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2
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3 This repository contains Galaxy tool wrappers for msconvert, part of
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4 the ProteoWizard (http://proteowizard.sourceforge.net/) package.
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5
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6 # Installing
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7
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8 Due to potential difficulties installing ProteoWizard with vendor
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9 library support, tools for interacting with vendor types are seperated
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10 out into their own wrappers. Galaxy is generally deployed under Linux,
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11 but vendor support in ProteoWizard requires .NET 4.0. There are at
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12 least two ways to get this to work:
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13
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14 * Galaxy jobs may be configured to submit to a Windows host with
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15 ProteoWizard installed using the
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16 LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR
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17
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18 * ProteoWizard can be installed under Wine. Guidance on how to set
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19 this up and package such environments for cloud deployments can be
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20 found here: https://github.com/jmchilton/proteomics-wine-env
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21
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22 Wrappers for both msconvert version 2 and version 3+ are provided
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23 because version 3+ of msconvert with vendor library support requires
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24 .NET 4.0 and this may difficult or impossible under Wine in Linux with
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25 all but the most recent versions of Wine (1.4+).
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26 # Obtaining Tools
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27
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28 Repositories for all Galaxy-P tools can be found at
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29 https:/bitbucket.org/galaxyp/.
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30
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31 # Contact
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32
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33 Please send suggestions for improvements and bug reports to
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34 jmchilton@gmail.com.
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35
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36 # License
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37
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38 All Galaxy-P tools are licensed under the Apache License Version 2.0
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39 unless otherwise documented.
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40
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41 # Tool Versioning
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42
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43 Galaxy-P tools will have versions of the form X.Y.Z. Versions
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44 differing only after the second decimal should be completely
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45 compatible with each other. Breaking changes should result in an
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46 increment of the number before and/or after the first decimal. All
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47 tools of version less than 1.0.0 should be considered beta.
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