sgssgene / raptor-galaxy

raptor-galaxy

This readme explains how to add a tool to bioconda and galaxy (by using planemo).

Bioconda

Bioconda has so called recipes for every available tool which are saved in their git repo https://github.com/bioconda/bioconda-recipes . To get your tool into bioconda you have to create a PR with a recipe for your tool. You can use the recipe of raptor as a template: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/raptor

Install and setup of planemo

The next 3 steps will install planemo into the directory .venv-planemo.

$ virtualenv .venv-planemo; source .venv-planemo/bin/activate
$ pip install "pip>=7"
$ pip install planemo

Each time you open a new console and want to use planemo, it is needed to activate the planemo environment:

$ source .venv-planemo/bin/activate

For more information on how to install planemo checkout the project https://github.com/galaxyproject/planemo .

Account on the toolshed

There exists the normal toolshed at https://toolshed.g2.bx.psu.edu/ and the test toolshed at https://testtoolshed.g2.bx.psu.edu/. The steps for both are the same. We will show here how to use the testtoolshed.

• create an account on https://testtoolshed.g2.bx.psu.edu
• run $ planemo config_init to create a planemo config
• insert shed_username and api key into ~/.planemo.yml

Creating a new description for a tool

Lets assume you want to add a new subcommand to raptor called newsubcommand.

• copy raptor-build.xml to raptor-newsubcommand.xml
• adjust the xml file to own needs
• run $ planemo test raptor-newsubcommand.xml to check tests
• run $ planemo lint raptor-newsubcommand.xml to lint

Publishing your tool

Make sure to bump the version number of the tool for every new release (see xml tag ).

• run $ planemo shed_update --shed_target testtoolshed path/to/this/repo to publish the tools of this repository