Question: deepvariant cannot import name locked_file
0
gravatar for 372910137
16 months ago by
3729101370
3729101370 wrote:

when i tried to install the DeepVariant (./build-prereq.sh) cannot import name locked_file

deepvariant genome • 532 views
ADD COMMENTlink modified 6 months ago by alaincoletta110 • written 16 months ago by 3729101370

You should directly follow up with google cloud genomics support. While Dr. DePristo seems to have joined Biostars I don't think he is going to provide regular support for deepvariant here.

ADD REPLYlink written 16 months ago by genomax65k

We implemented the DeepVariant pipeline with Docker and Nextflow. You can try it here https://lifebit.page.link/gnbR with example parameters.

There is also a post with benchmarks across various AWS instances here: https://blog.lifebit.ai/post/deepvariant/.

ADD REPLYlink written 6 months ago by alaincoletta110

Tagging: arostami

ADD REPLYlink written 16 months ago by genomax65k

Hi Mark, we implemented the DeepVariant pipeline with Docker and Nextflow here

Lifebit integrate it the pipeline with example parameters

Would love your feedback on this.

Thanks!

ADD REPLYlink modified 6 months ago • written 6 months ago by alaincoletta110
1
gravatar for mdepristo
16 months ago by
mdepristo60
mdepristo60 wrote:

First, it's better if you tag these posts with deepvariant so we get pinged by biostars that people are asking about DeepVariant. Second, I'd recommend you post this as an issue on github repo: https://github.com/google/deepvariant/issues with a bunch more details so we can reproduce and fix.

ADD COMMENTlink written 16 months ago by mdepristo60

Just thought to let you know... Saddly, the "watched tag" feature of biostars is there but it doesn't work (see Biostars meta: Does "Watched tags" work? ). (If it works for you let me know, please!)

ADD REPLYlink modified 16 months ago • written 16 months ago by dariober10.0k
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