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HenrikBengtsson / CBI-software

A Scientific Software Stack for HPC (CentOS oriented)
https://wynton.ucsf.edu/hpc/software/software-repositories.html
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picard: rename 'picard' to 'PicardCommandLine': #69

Closed HenrikBengtsson closed 2 years ago

HenrikBengtsson commented 2 years ago

Only noticed this now, but the help mentions PicardCommandLine;

$ java -jar "$PICARD_HOME/picard.jar" PicardCommandLine --help
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch/henrik
USAGE: PicardCommandLine <program name> [-h]

Available Programs:
...

It seems more natural to use PicardCommandLine than our own picard. Will probably have to keep the latter, but it should be deprecated.