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deepvariant: conda environment not installable #2296

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votti opened this issue Nov 7, 2023 · 1 comment
Open

deepvariant: conda environment not installable #2296

votti opened this issue Nov 7, 2023 · 1 comment
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@votti
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votti commented Nov 7, 2023

Snakemake version

  • snakemake: 7.32.4
  • snakemake_warppers: master/v2.9.1

Describe the bug
Currently the conda environment associdated with the deepvariant wrapper cannot be installed.

Logs

(snakemake) xxxx:~/Git/snakemake-wrappers/bio/deepvariant/test$ snakemake -c 6 --use-conda gvcf_calls/a.g.vcf.gz
Building DAG of jobs...
Creating conda environment https://github.com/snakemake/snakemake-wrappers/raw/master/bio/deepvariant/environment.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /tmp/tmpk97jy7tx.yaml:
Command:
mamba env create --quiet --file "/home/vitoz/Git/snakemake-wrappers/bio/deepvariant/test/.snakemake/conda/47ab421ca857ecac810448669a2010ab_.yaml" --prefix "/home/vitoz/Git/snakemake-wrappers/bio/deepvariant/test/.snakemake/conda/47ab421ca857ecac810448669a2010ab_"
Output:
Could not solve for environment specs
The following package could not be installed
└─ deepvariant 1.4**  is uninstallable because it requires
   └─ tensorflow-estimator 2.0.* , which does not exist (perhaps a missing channel).

Minimal example

cd snakemake-wrappers/bio/deepvariant/test
snakemake -c 6 --use-conda gvcf_calls/a.g.vcf.gz

Additional context
Run on Ubuntu 23.04

@fgvieira
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fgvieira commented Dec 1, 2023

It seems to be a bioconda issue.
But it has been already reported in google/deepvariant#736 and they claim it is working.

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