Conda only environments - remove singularity dependency

[douglowe]

Two chunks of work:

1) Conda channel lists standardised to priority list: conda-forge -> bioconda -> defaults

2) blobtool dependencies switched away from singularity to a conda/pip environment

[elichad]

I am testing this, but it's taking ages to run the pipeline. Not sure why - I thought the first time it might be updating the environments, but I'm running it a second time and it's still slow.

[elichad]

CreateCondaEnvironmentException:
Could not create conda environment from /home/eli/manchester/bge-hack/skim2mt/workflow/rules/../envs/mafft.yaml:
Command:
mamba env create --quiet --file "/home/eli/manchester/bge-hack/skim2mt/.snakemake/conda/f5b2acb6bf3083f7299b30cbbbc760e7_.yaml" --prefix "/home/eli/manchester/bge-hack/skim2mt/.snakemake/conda/f5b2acb6bf3083f7299b30cbbbc760e7_"
Output:
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package mafft-7.508-hec16e2b_0 is excluded by strict repo priority
  - 

[douglowe]

@elichad - has setting channel priority to flexible solved the problem for you?

[douglowe]

great :)

[o-william-white]

Thanks :)