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UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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RELEASE: lg3 2021-10-08 #162

Closed HenrikBengtsson closed 2 years ago

HenrikBengtsson commented 2 years ago

FYI, I've created lg3 2021-10-08, which is a fork of the previous release 2020-05-26. The updates are https://github.com/UCSF-Costello-Lab/LG3_Pipeline/compare/2020-05-26..2021-10-08.

The main thing with this new version is that one can now override the default software tools that are (still) hard-coded in the pipeline with custom once using environment variables. These environment variables can be set in a local ./lg3.conf. See https://github.com/UCSF-Costello-Lab/LG3_Pipeline/blob/next-release/examples/configs/modules/lg3.conf for validated example.

I think this is the first major step towards making it possible for end-users to run the pipeline, including on C4. The reference files are still hosted on the TIPCC file system, but since that is also mounted on C4 as-is, I have hopes that on can run lg3 2021-10-08 also from C4. I will try this next.

HenrikBengtsson commented 2 years ago

I have hopes that on can run lg3 2021-10-08 also from C4. I will try this next.

Silly me. I forgot that C4 does not use Torque/PBS, so all those commands need to be updated to make use of Slurm.

HenrikBengtsson commented 2 years ago

I see you've done lots of this already:

https://github.com/UCSF-Costello-Lab/LG3_Pipeline/blob/0005423f801bbf7f01c0b083670717a7a8538ff2/runs_demo/_run_Trim#L68-L77

vs

https://github.com/UCSF-Costello-Lab/LG3_Pipeline/blob/2e616a3d2e3455859834843d8982fe31e16e0ff3/runs_demo/_run_Trim#L82-L83

HenrikBengtsson commented 2 years ago

Turns out #163 was enough to get it running on C4. No need to rewrite the code to use Slurm commands.