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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:51:45 -0400
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487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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1 Mascot
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2 ======
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487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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4 Galaxy wrapper for the Mascot_ tandem ms search tool and a tool to convert results to `pepXML`
487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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6 .. _Mascot: http://www.matrixscience.com/
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487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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8 Requirements
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9 ------------
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487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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11 This package uses protk_, and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. In addition, you will need a working installation of Mascot_ which is commercial software.
487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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13 .. _protk: https://github.com/iracooke/protk
487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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14 .. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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17 There are two ways you can satify these dependencies (choose one):
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19 1. **Manual Install:** Details on how to install protk_, msgfplus_ and Proteowizard_ manually are available here_.
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487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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21 2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed.
487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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23 .. _docker: https://www.docker.com/
487533fa6990 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
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24 .. _here: https://github.com/iracooke/protk/#galaxy-integration
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25 .. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
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26 __ container_
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29 Further Info
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30 ------------
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32 The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__
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34 .. _github: https://github.com/iracooke/protk-galaxytools
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35 .. _issue: https://github.com/iracooke/protk-galaxytools/issues
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36 __ issue_