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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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[BUG] rgi is uninstallable with mamba / snakemake #225

Closed hazmup closed 1 year ago

hazmup commented 1 year ago

I am trying to use rgi in a snakemake pipeline that creates a dedicated rgi environment.

This is the env config file I am using:

channels:
  - bioconda
  - conda-forge
dependencies:
  - rgi = 6.0.2

I tried installing on a regular conda env and got the same error with more detail. I have tried installing the latest version of mambaforge and snakemake fresh.

When running the pipeline I am getting the following:

CreateCondaEnvironmentException:
Could not create conda environment from envs/rgi.yaml:
Command:
mamba env create --quiet --file ".snakemake/conda/f3d6759e159ec196e8194997c9a3badd_.yaml" --prefix "snakemake/conda/f3d6759e159ec196e8194997c9a3badd_"
Output:
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following package could not be installed
└─ rgi 6.0.2**  is uninstallable because it requires
   └─ biopython 1.78.* , which conflicts with any installable versions previously reported.

Before updating mambaforge I was getting a different error, which was:
CreateCondaEnvironmentException:
Could not create conda environment from /users/pa22/sgkionis/envs/rgi.yaml:
Command:
mamba env create --quiet --file "/users/pa22/sgkionis/.snakemake/conda/5c021401d755900074c6e4e5ddab192f_.yaml" --prefix "/users/pa22/sgkionis/.snakemake/conda/5c021401d755900074c6e4e5ddab192f_"
Output:
Could not solve for environment specs
Encountered problems while solving:
  - package rgi-6.0.2-pyha8f3691_0 requires lxml 4.6.5, but none of the providers can be installed

The environment can't be solved, aborting the operation

This is on a computer cluster running SLURM.