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"planemo upload commit 79f62a93f1c45ae643ce01ff3dcf9662c304c11b-dirty"
author gene
date Mon, 04 Oct 2021 09:54:45 +0000
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1 # raptor-galaxy
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2
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3 This readme explains how to add a tool to bioconda and galaxy (by using planemo).
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4
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5 ## Bioconda
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6 Bioconda has so called recipes for every available tool which are saved in their git repo https://github.com/bioconda/bioconda-recipes .
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7 To get your tool into bioconda you have to create a PR with a recipe for your tool.
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8 You can use the recipe of raptor as a template: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/raptor
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9
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10 ## Install and setup of planemo
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11 The next 3 steps will install planemo into the directory `.venv-planemo`.
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12 ```
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13 $ virtualenv .venv-planemo; source .venv-planemo/bin/activate
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14 $ pip install "pip>=7"
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15 $ pip install planemo
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16 ```
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17 Each time you open a new console and want to use planemo, it is needed to activate the planemo environment:
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18 ```
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19 $ source .venv-planemo/bin/activate
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20 ```
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21 For more information on how to install planemo checkout the project https://github.com/galaxyproject/planemo .
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24 ## Account on the toolshed
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25 There exists the normal toolshed at https://toolshed.g2.bx.psu.edu/ and the test toolshed at https://testtoolshed.g2.bx.psu.edu/.
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26 The steps for both are the same. We will show here how to use the testtoolshed.
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27 - create an account on https://testtoolshed.g2.bx.psu.edu
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28 - run `$ planemo config_init` to create a planemo config
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29 - insert shed_username and api key into ~/.planemo.yml
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31 ## Creating a new description for a tool
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32 Lets assume you want to add a new subcommand to raptor called `newsubcommand`.
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33 - copy raptor-build.xml to raptor-newsubcommand.xml
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34 - adjust the xml file to own needs
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35 - run `$ planemo test raptor-newsubcommand.xml` to check tests
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36 - run `$ planemo lint raptor-newsubcommand.xml` to lint
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38 ## Publishing your tool
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39 Make sure to bump the version number of the tool for every new release (see xml tag <tool version="..."> ).
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40 - run `$ planemo shed_update --shed_target testtoolshed path/to/this/repo` to publish the tools of this repository