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caozhichongchong / QuickVariants

Fast and Accurate Variant Identification Tool for Sequencing-Based Studies
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Support for conda envs #2

Closed RonaldOellers closed 2 months ago

RonaldOellers commented 7 months ago

Hey, I am new to adding .jar files to a conda env.

From your README, you seem to not have packaged it into any of the repositories. How would you add this to a conda env? or otherwise bind into a workflow? I want to test wether this might perform better in my pipeline that bcftools call.

Thank you for this very interesting new tool!

caozhichongchong commented 7 months ago

Hi,

Interesting question.

You can activate your conda environment where you intend to run QuickVariants. Then you can install java by conda install conda-forge::openjdk After installation, you can execute the QuickVariants JAR file you downloaded from here by running java -jar quick-variants.jar <arguments> Please let us know if you have any questions. Thank you.

RonaldOellers commented 7 months ago

Hey, I would look to see if I can put it into a snakemake workflow, so I need to be able to have a environment defined where it is installed in. Ideally automatically via eg. a conda env.yml. The running part seems clear and easy to use

caozhichongchong commented 7 months ago

Hi,

I see. You may now install both java and QuickVariants by conda install caozhichongchong::quick-variants QuickVariants can be found at $Conda_env_location/bin/quick-variants-VERSION.jar QuickVariants can be run by java -jar $Conda_env_location/bin/quick-variants-VERSION.jar <arguments> Thanks.

mathjeff commented 2 months ago

Thanks everybody! I think this is done now