dockstore-biobambam2 is a dockstore.org wrapper for the tools of biobambam2. This has been packaged specifically for use with the Dockstore.org framework.
This repository includes the Dockerfile directives and a suite of cwl files describing each tool.
It is a work in progress and tools will be added:
- As CancerIT require them for tools we want to expose via dockstore.org.
- Contribution via Pull requests.
- Requests made via Issues.
- bamtofastq - dockstore-biobambam2/bamtofastq
Requires dockstore cli version 1.2.3+
This project uses git pre-commit hooks. As these will execute on your system you need to activate them. Failure to adhere to these may result in rejection of your work.
You will need to install:
gem install --user-install mdl
The following command will activate the checks to execute before a commit is processed:
git config core.hooksPath git-hooks
A failure will block a commit, this includes style for terraform.
You can run the same checks manually without a commit by executing the following in the base of the clone:
./run_checks.shUnfortunately biobambam2 takes ~45 minutes to build which prevents travis-CI for the project as the max total time is 50 min.