Comments (4)
Hi @lynnjo,
You may check PacBio case study which uses Conda.
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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
from deepvariant.
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.
from deepvariant.
Hi @lynnjo , as @akolesnikov mentioned, we don't officially support Conda. I'll close this issue now.
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