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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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