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auerlab / ad2vcf

Add allelic depth info from a SAM stream to a VCF file
BSD 2-Clause "Simplified" License
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Containerized ad2vcf #5

Closed jonathonl closed 6 months ago

jonathonl commented 6 months ago

Would it be possible for you to provide a Singularity container or Docker image for ad2vcf? FreeBSD isn't an option for us and the non-FreeBSD instructions are not working. After installing Pkgsrc (selected "current" and default prefix), the ~/Pkgsrc/biology/ad2vcf does not exist.

outpaddling commented 6 months ago

No, there is no reason to containerize this software. Containers are often used as an alternative to understanding and fixing build issues, but doing the latter should be simple here. All of the software here is well-tested on multiple BSDs, Linux distros and macOS using pkgsrc. I'd be happy to help you troubleshoot any issues you're having with pkgsrc.

First, did you mean to write ~/Pkgsrc/pkgsrc/biology/ad2vcf?

jonathonl commented 6 months ago

No, the path I referenced is what I meant to write. I'm following instructions at https://github.com/auerlab/ad2vcf/blob/e84275be567fefed5f3f8f0192bac8c8806210ff/README.md?plain=1#L124-L126

outpaddling commented 6 months ago

I see... That's a typo that has apparently been in a few of my repos since the beginning, and nobody ever mentioned before. It's fixed now. Let me know if you run into any other issues. Thanks for the heads-up.