As the name suggests, these are tools that should be ready to use "out of the box" with no code modifications. As such, there are two reasonable ways to use them.
- Make a personal copy of the script(s) you want to use and place them in your ~/bin directory
- Place a symbolic link to the script(s) you want to use into your ~/bin directory
These will accomplish almost the same thing in terms of usability. The only difference is that if changes are made to the version of the script in this collection, only method 2 will propagate them to you immediately. This can be good if you want to stay as up-to-date as possible, but can also lead to unexpected changes in your analyses.
As the name suggests, these are code notebooks that are meant to be tailored to purpose for each individual dataset and analysis they are run on. As such, you should always make a copy of these workbooks in the directory for your specific analysis and only make changes to your personal copies.
In many cases, it may be better to find a similar notebook from a recently run analysis and use that as your starting point instead of these references. This repository is updated relatively infrequently, so if there are improvements made to the workflow by individual lab members it may take a while for those changes to make it into this collection.
If you think you have a script that might make other people's lives easier, consider adding it to this collection. If you think a script in this collection needs improvements or is out of date, consider how to edit it. There is probably someone in the lab who is the bioinformatics point person; check with them before modifying any part of this repository or if you want to push your update to the lab's GitHub repository for useful scripts.