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broadinstitute / picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
https://broadinstitute.github.io/picard/
MIT License
967 stars 370 forks source link

Picard should have a version command #1289

Open bartgrantham opened 5 years ago

bartgrantham commented 5 years ago

I feel ridiculous even asking this question, but how can I tell what version of Picard I'm running? I'm using the broadinstitute/picard:latest docker image and because of it's ambiguous tagging I need to tag it locally... but I can't figure out how to do that from invoking picard itself.

-h, -v, and --version aren't recognized (after figuring out that the docker helper script was getting in the way), there's no "Version" subcommand... I can't figure it out.

The ANSI colors on the usage page are a nice touch, but simple information like version is better.

cmnbroad commented 5 years ago

Picard will include the version in the output if you specify the name of a tool to run, with either "-h" or with no additional args:

java -jar .... SortSam -h

but I agree there should be a more intuitive way.

bartgrantham commented 5 years ago

Thank you for changing the title. :) I was thinking that this was a missing feature of such importance it borders on a bug.