Running with Conda

[lynnjo]

Running with Conda

[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.