Currently MCODE can be used to create clusters for AutoAnnotate, but it has to be done manually by the user. The idea is to be able to run MCODE programatically just like how we use clusterMaker.
Detect if MCODE is installed (how?) and if so provide an option to use it in the Advanced tab of the creation dialog.
If MCODE is not installed provide the user with a link to go install it (like we do with clusterMaker)
Note: MCODE will not be a hard dependency like clusterMaker, purely optional, the user will just be nudged into downloading it.
This may require some changes in the MCODE app. I will have to look at what commands it provides. I would like to use it for clustering but not have the MCODE panels show up.
Add MCODE to the EnrichmentMap Pipeline Collection meta-app.
Improve integration with the MCODE app.
Currently MCODE can be used to create clusters for AutoAnnotate, but it has to be done manually by the user. The idea is to be able to run MCODE programatically just like how we use clusterMaker.