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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 #90

Closed HenrikBengtsson closed 5 years ago

HenrikBengtsson commented 5 years ago

I'm ready for doing another release with the following updated:

Version 2018-10-11-9000

SIGNIFICANT CHANGES

Environment variable 'LG3_HOME' must now be set. If not set, an error is produced. It used to default to a Costello Lab specific location on the TIPCC cluster.

NEW FEATURES

Alignment jobs now require less memory by default (64 GiB RAM instead of 100 GiB), which should decreased the average default queuing time.
Added lg3 envir for displaying current environment variables related to the LG3 Pipeline.
Added lg3 --news for displaying the NEWS.md file in the terminal.

KNOWN ISSUES

Patient IDs must not contain underscores ('_') because the Pindel step of the pipeline does not support that. All steps of the pipeline now assert that patient IDs do no contain underscores.

BUG FIXES

PBS scripts would only run on TIPCC compute nodes that support the legacy PBS bigmem flag. By removing this unnecessay bigmem requirement from all PBS scripts, jobs can now run on all compute nodes that meet the core and memory requirement specified by each PBS script (or is overridden in the LG3 call).

@ivan108, ok with you?

ivan108 commented 5 years ago

Great! OK with me.

HenrikBengtsson commented 5 years ago

New version released and deployed on TIPCC;

[cbctest2@cclc01 ~]$ module load CBC lg3
l[cbctest2@cclc01 ~]$ lg3 --version
2018-10-17
l[cbctest2@cclc01 ~]$

/cc @shuntsman-ucsf