Running with Conda

[lynnjo]

Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md: Yes Describe the issue: This isn't a code problem, but rather a documentation issue. I've run DeepVariant via your docker with success. To integrate it with our project I would like to install it via conda. I was able to do that but it isn't clear how to run deep variant. Do you have documentation/examples of what commands to send?

When using docker, we invoke the google/deepvariant:1.6.1 image and send it the command "/opt/deepvariant/bin/run_deepvariant" with appropriate arguments. What do we run when using conda?

Note the docs/deepvariant-quick-start.md has examples for docker (very useful and they work with our data) but nothing for conda.

Setup

• Operating system: linux
• DeepVariant version: 1.5.0 (latest from conda)
• Installation method (Docker, built from source, etc.): conda
• Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?)

Steps to reproduce:

• Command:
• Error trace: (if applicable)

Does the quick start test work on your system? Please test with https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md. Is there any way to reproduce the issue by using the quick start?

Any additional context:

Do you have plans to update conda with the latest deepvariant version? It is still at 1.5.0. Thanks

[akolesnikov]

Hi @lynnjo,

You may check PacBio case study which uses Conda.

[lynnjo]

Thanks for the response @akolesnikov . I must be missing something. From your PacBio case study link above, I see conda being used to setup samtools, but deepvariant is still run via singularity. Is it possible to run deepvariant only through conda, or is docker/singularity always required?

singularity exec --bind /usr/lib/locale/ \ docker://google/deepvariant:${BIN_VERSION} \ /opt/deepvariant/bin/run_deepvariant \ --model_type PACBIO \ --ref reference/GRCh38_no_alt_analysis_set.fasta \ --reads input/HG003.GRCh38.chr20.pFDA_truthv2.bam \ --output_vcf deepvariant_output/output.vcf.gz \ --num_shards $(nproc) \ --regions chr20

[akolesnikov]

Please refer to this issue that contains some information on Conda. Unfortunately, we don't support Conda and there is no documentation on how to install through Conda.

[pichuan]

Hi @lynnjo , as @akolesnikov mentioned, we don't officially support Conda. I'll close this issue now.