Recent work on the Pachyderm-Annotations repo has resulted in the annotations being updated without regenerating PharmacoSets or re-running the gene signature pipelines. While continuous improvement of our annotations is an obvious good, it keeps breaking the pipeline and wasting a lot of my time.
As a result we need to (1) improve lab SOPs to ensure that updates to annotations/PharmacoSets and gene signature files occur in the correct order and nearly the same time or (2) formalize mechanisms for renaming updated annotations as part of the PharmacoDI pipeline.
Given that the code is partially implemented already, (2) is likely preferable.
To find these work arounds, use CTRL + F to search for "##FIXME:: " tags in the the code comments. These should be removed ASAP.
Recent work on the Pachyderm-Annotations repo has resulted in the annotations being updated without regenerating PharmacoSets or re-running the gene signature pipelines. While continuous improvement of our annotations is an obvious good, it keeps breaking the pipeline and wasting a lot of my time.
As a result we need to (1) improve lab SOPs to ensure that updates to annotations/
PharmacoSets and gene signature files occur in the correct order and nearly the same time or (2) formalize mechanisms for renaming updated annotations as part of the PharmacoDI pipeline.Given that the code is partially implemented already, (2) is likely preferable.
To find these work arounds, use CTRL + F to search for "##FIXME:: " tags in the the code comments. These should be removed ASAP.