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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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Next release #72

Closed HenrikBengtsson closed 6 years ago

HenrikBengtsson commented 6 years ago

It looks like we're soon ready for the next release.

I'm running final tests on Patient157t10 with neither LG3_OUTPUT_ROOT nor LG3_INPUT_ROOT set. That should complete later tonight (Sunday). After that, I think we can release the next version. @ivan108, ok with you?

HenrikBengtsson commented 6 years ago

I'm done with all my tests. Everything looks good.

ivan108 commented 6 years ago

Great work! Go ahead with the release. I was off the grid on the weekend, will do some testing today.

HenrikBengtsson commented 6 years ago

LG3_Pipeline 2018-10-08 released:

$ module load CBC lg3
$ lg3
LG3 Pipeline

Usage:
 lg3 <tool> ...

Tools:
 cleanup   Selectively Delete LG3 Pipeline Output
 status    Check Status of Running LG3 Pipeline
 test      Run and Validate LG3 Pipeline Test Examples

Examples:
 lg3 --help
 lg3 --version
 lg3 status --help
 lg3 status --all Patient157t
 lg3 cleanup --help
 lg3 test setup
 lg3 test validate Patient157t

Settings:
 LG3_HOME=/home/shared/cbc/software_cbc/LG3_Pipeline-2018-10-08
 EMAIL=

Version: 2018-10-08
Source: https://github.com/UCSF-Costello-Lab/LG3_Pipeline
HenrikBengtsson commented 6 years ago

@shuntsman-ucsf, FYI, we're released LG3_Pipeline v2018-10-08, which module load lg3 now defaults to. Nothing has changed in the trimming step, so this should not affect whatever you've already launched. But please make sure to start/continue in a fresh terminal on TIPCC going forward.

We've also simplified and improved the README, so make sure you don't follow the previous instructions.