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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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just FYI, for those who want to develop or debug Pisces on Linux.. #58

Open tamsen opened 3 years ago

tamsen commented 3 years ago

For those interested interested in doing their own debugging or dev work on Pisces and you don't have windows, I have a not-official-illumina-release personal fork with a more Linux-friendly version of Pisces available. This version does not require dotnet to be installed as a pre-req to running Pisces, and supports development & debugging on Linux OS. (I have been using Visual Studio Code 1.43.2 on Ubuntu and it seems really nice..)

repo : https://github.com/tamsen/Pisces/ latest binaries : https://github.com/tamsen/Pisces/releases/tag/v5.3.0.0 wiki: https://github.com/tamsen/Pisces/wiki

best Tamsen

stephanflemming commented 3 years ago

Is there a reason why the bioconda recipe is still on 5.2.10.49 ?

https://bioconda.github.io/recipes/pisces/README.html

tamsen commented 3 years ago

I didn't personally set any of the Pisces/conda integration up, but presumably b/c that is the latest release on the fork conda is tracking. 5.2.10.49 is the most recent official illumina version.

bgruening commented 3 years ago

@tamsen if we want to include this tool in Galaxy (galaxyproject.org) to you recommend your fork or should we work with the stable version. Our users mainly use HPC and Linux-based clouds.

tamsen commented 3 years ago

I recommend my fork. Should be much more friendly and stable for HPC and Linux.

bgruening commented 3 years ago

Ok cool, then we would try to update the Bioconda recipe pointing to your fork. Thanks.