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author galaxyp
date Fri, 26 Sep 2014 14:44:54 -0400
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1 # msconvert 1 GalaxyP - ProteoWizard msconvert
2 ================================
2 3
3 This repository contains Galaxy tool wrappers for msconvert, part of 4 * Home: <https://bitbucket.org/galaxyp/msconvert>
4 the ProteoWizard (http://proteowizard.sourceforge.net/) package. 5 * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert>
6 * Tool ID: `msconvert`
5 7
6 # Installing
7 8
8 Due to potential difficulties installing ProteoWizard with vendor 9 Description
9 library support, tools for interacting with vendor types are seperated 10 -----------
10 out into their own wrappers. Galaxy is generally deployed under Linux,
11 but vendor support in ProteoWizard requires .NET 4.0. There are at
12 least two ways to get this to work:
13 11
14 * Galaxy jobs may be configured to submit to a Windows host with 12 msconvert from ProteoWizard.
15 ProteoWizard installed using the
16 LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR
17 13
18 * ProteoWizard can be installed under Wine. Guidance on how to set 14 Note: This requires manual installation of ProteoWizard, and may require a Windows environment.
19 this up and package such environments for cloud deployments can be
20 found here: https://github.com/jmchilton/proteomics-wine-env
21 15
22 Wrappers for both msconvert version 2 and version 3+ are provided 16 See:
23 because version 3+ of msconvert with vendor library support requires
24 .NET 4.0 and this may difficult or impossible under Wine in Linux with
25 all but the most recent versions of Wine (1.4+).
26 # Obtaining Tools
27 17
28 Repositories for all Galaxy-P tools can be found at 18 * <http://proteowizard.sourceforge.net/>
29 https:/bitbucket.org/galaxyp/. 19 * <http://proteowizard.sourceforge.net/tools/msconvert.html>
30 20
31 # Contact
32 21
33 Please send suggestions for improvements and bug reports to 22 Installing
34 jmchilton@gmail.com. 23 ----------
35 24
36 # License 25 Due to potential difficulties installing ProteoWizard with vendor library support, tools for interacting with vendor types are seperated out into their own wrappers. Galaxy is generally deployed under Linux, but vendor support in ProteoWizard requires .NET 4.0. There are at least two ways to get this to work:
37 26
38 All Galaxy-P tools are licensed under the Apache License Version 2.0 27 * Galaxy jobs may be configured to submit to a Windows host with ProteoWizard installed using the [LWR](https://wiki.g2.bx.psu.edu/Admin/Config/LWR).
39 unless otherwise documented.
40 28
41 # Tool Versioning 29 * ProteoWizard can be installed under Wine. Guidance on how to set this up and package such environments for cloud deployments can be found here: <https://github.com/jmchilton/proteomics-wine-env>
42 30
43 Galaxy-P tools will have versions of the form X.Y.Z. Versions 31
44 differing only after the second decimal should be completely 32 GalaxyP Community
45 compatible with each other. Breaking changes should result in an 33 -----------------
46 increment of the number before and/or after the first decimal. All 34
47 tools of version less than 1.0.0 should be considered beta. 35 Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
36
37 <https://bitbucket.org/galaxyp/galaxyp>
38
39
40 License
41 -------
42
43 Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
44
45 To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
46
47 You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
48
49 You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
50
51
52 Contributing
53 ------------
54
55 Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
56
57
58 Authors
59 -------
60
61 Authors and contributors:
62
63 * Björn Grüning
64 * Cody Wang
65 * Fred Sadler
66 * John Chilton <jmchilton@gmail.com>
67 * Minnesota Supercomputing Institute, Univeristy of Minnesota