Mercurial > repos > gene > raptor_seqan3
comparison README.md @ 0:bbdc3fdf5298 draft default tip
"planemo upload commit 79f62a93f1c45ae643ce01ff3dcf9662c304c11b-dirty"
| author | gene |
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| date | Mon, 04 Oct 2021 09:54:45 +0000 |
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| 1 # raptor-galaxy | |
| 2 | |
| 3 This readme explains how to add a tool to bioconda and galaxy (by using planemo). | |
| 4 | |
| 5 ## Bioconda | |
| 6 Bioconda has so called recipes for every available tool which are saved in their git repo https://github.com/bioconda/bioconda-recipes . | |
| 7 To get your tool into bioconda you have to create a PR with a recipe for your tool. | |
| 8 You can use the recipe of raptor as a template: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/raptor | |
| 9 | |
| 10 ## Install and setup of planemo | |
| 11 The next 3 steps will install planemo into the directory `.venv-planemo`. | |
| 12 ``` | |
| 13 $ virtualenv .venv-planemo; source .venv-planemo/bin/activate | |
| 14 $ pip install "pip>=7" | |
| 15 $ pip install planemo | |
| 16 ``` | |
| 17 Each time you open a new console and want to use planemo, it is needed to activate the planemo environment: | |
| 18 ``` | |
| 19 $ source .venv-planemo/bin/activate | |
| 20 ``` | |
| 21 For more information on how to install planemo checkout the project https://github.com/galaxyproject/planemo . | |
| 22 | |
| 23 | |
| 24 ## Account on the toolshed | |
| 25 There exists the normal toolshed at https://toolshed.g2.bx.psu.edu/ and the test toolshed at https://testtoolshed.g2.bx.psu.edu/. | |
| 26 The steps for both are the same. We will show here how to use the testtoolshed. | |
| 27 - create an account on https://testtoolshed.g2.bx.psu.edu | |
| 28 - run `$ planemo config_init` to create a planemo config | |
| 29 - insert shed_username and api key into ~/.planemo.yml | |
| 30 | |
| 31 ## Creating a new description for a tool | |
| 32 Lets assume you want to add a new subcommand to raptor called `newsubcommand`. | |
| 33 - copy raptor-build.xml to raptor-newsubcommand.xml | |
| 34 - adjust the xml file to own needs | |
| 35 - run `$ planemo test raptor-newsubcommand.xml` to check tests | |
| 36 - run `$ planemo lint raptor-newsubcommand.xml` to lint | |
| 37 | |
| 38 ## Publishing your tool | |
| 39 Make sure to bump the version number of the tool for every new release (see xml tag <tool version="..."> ). | |
| 40 - run `$ planemo shed_update --shed_target testtoolshed path/to/this/repo` to publish the tools of this repository |