search

PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
Other
258 stars 71 forks source link

Feature request: `--version` command line option #586

Open scwatts opened 2 years ago

scwatts commented 2 years ago

It would be useful to have a --version option available for the gridss script to easily obtain version information. As far as I've seen the version is only provided in filenames e.g. gridss-2.13.2-gridss-jar-with-dependencies.jar

d-cameron commented 2 years ago

So essentially, a more user friendly wrapper around the --version command line argument available within the jar itself, correct?

$ java -cp gridss-2.13.2-gridss-jar-with-dependencies.jar gridss.CallVariants --version
2.13.2-gridss
scwatts commented 2 years ago

Thanks for pointing that out. I missed it in the GRIDSS codebase - looks like the code for the --version option called is from org.broadinstitute.barclay.argparser via picard.cmdline.CommandLineProgram.

A more user friendly way to obtain GRIDSS version would be great. I understand that GRIDSS is architected in a way that requires the gridss script to be provided the GRIDSS JAR path, so it might seem somewhat circular to have a --version option when the JAR filename contains the version already. However, the Conda GRIDSS package (and Biocontainer Docker image) provides an accompanying wrapper script that is placed in PATH and automatically sets the --jar argument for the gridss script. Having a --version option in these instances would be particularly useful.

Ideally we could obtain version information with:

$ gridss --version
2.13.2-gridss