bionitio
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Demonstrating best practices for bioinformatics command line tools
Having a `.gitignore` file is important - it prevents people from accidentally committing files to the git repository (I'm looking at you, OSX `.DS_Store` 👀 ). `.gitignore` files are typically...
GitHub [recently added](https://github.blog/2019-06-06-generate-new-repositories-with-repository-templates/) a new repository setting to mark a repo as a "template repository". It's quite easy to set up (see [docs](https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-template-repository)) and basically just [adds a little badge](https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-repository-from-a-template)...
Your setup in the python template probably wont work if the user doesnt have setuptools installed. which is actually common. Something like this in setup.py would be good: ``` try:...
Consider using GitHub actions instead of Travis
Currently the bionitio-boot.sh script uses curl to communicate with the GitHub API. Password authentication via this API is being deprecated and the recommendation from GitHub is to use a personal...
We could mount in the functional_tests directory, so that it doesn't have to be part of the Docker image itself (like it is now). However this would mean the users...
A user has reported that GitHub integration failed on Windows under PowerShell. Running the bootstrap script: - a new/different command-line window was opened - this asked for the user's GitHub...
At the moment, behaviour is inconsistent if the input file exists, but is not a fasta file. I suspect the program should exit with a nonzero exit status in this...
Using the Python mode, I found that if the expected file was missing that the test still passes. The line starting with "diff" indicates a file is missing, but the...
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Demonstrating best practices for bioinformatics command line tools