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ncbi / sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
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Source release? #1

Closed olsonanl closed 3 years ago

olsonanl commented 3 years ago

Hi- I am interested in evaluating this tool but cannot run docker in our production environment and there doesn't appear to be a release available here. Will one be coming out soon?

Thanks, Bob Olson ANL

multikengineer commented 3 years ago

@olsonanl my apologies. I have pushed an initial feature branch, and will create a master branch tomorrow. Bob - can you run a singularity container in your production env?

olsonanl commented 3 years ago

Great - thank you. Yes, we use singularity extensively in our cluster.

I did build a singularity container from the docker version; however, our production nodes are still running CentOS 6 and the resulting container isn't compatible with C6.

multikengineer commented 3 years ago

Thanks Bob.. Yes, the container was build on Debian. I can somewhat easily build it on a centos7 host (and see that it works). It would not be easy for me to build it on centos6, let alone getting approval to do so. Any chance your nodes might get upgraded soon?

olsonanl commented 3 years ago

It’s in plan. If you have the sources such that I can build from scratch I should be able to build out the tool in my environment (I have a large collection of bioinformatic software already in place here).

multikengineer commented 3 years ago

You can see the repo has scripts, and a binary compiled app. It is possible to in fact build that binary from a different repo (nfs-tools) if the binary won't run on your host.

olsonanl commented 3 years ago

Cool. I will give this a shot this week and let you know how it goes