3. Developers: Contribute to bionitio

This page is under development

The Bionitio tool sets up a template for tools in various languages.

• Bionitio projects can be set up for various languages, and modified to do bioinformatics tasks.

• This is what we have covered in the wiki page: Set up a project with bionitio.

However, if you want to modify the actual overall Bionitio tool itself, this page provides extra instructions.

The structure of bionitio

Repository: https://github.com/bionitio-team

Main folder: https://github.com/bionitio-team/bionitio

There are also folders for each language: https://github.com/bionitio-team/bionitio-c
https://github.com/bionitio-team/bionitio-rust etc.

Get the code

Clone all the folders - the main bionitio folder and then the ones for each of the languages.

Clone all the repositories using the bionitio git wrapper:

bs=$BIONITIO_SRC
mkdir $SCRATCH_DIR
cd $SCRATCH_DIR
${bs}/githelper/bionitio-git.sh -c clone

Or, if you already have cloned the repositories, then you can pull their updates:

${bs}/githelper/bionitio-git.sh -c pull 

Note: if you want to also clone the subfolder of functional tests, add in --recurse-submodules to the git clone command.

Make changes

Example: making changes to the README files for each language.

The README for each language is built from a template, plus extra language-specific information. This information is held in several files within language/readme_includes folder, such as help.md, install.md etc.

For example, installation instructions for clojure are in the bionitio-clojure/readme_includes/install.md file.

Modify these separately for each language where required.

Note: If you are adding a file, you will need to git add these files, e.g to add a file called errors.md:

$ for file in bionitio-*; do (cd $file; git add readme_includes/errors.md) done

If you have modified a file only, you can git commit the changes, follow the instructions here.