diff --git a/envs/chewbbaca.yaml b/envs/chewbbaca.yaml index 07c5984..4ac59ce 100644 --- a/envs/chewbbaca.yaml +++ b/envs/chewbbaca.yaml @@ -2,6 +2,7 @@ name: chewbbaca channels: - bioconda - conda-forge + - nodefaults dependencies: - chewbbaca=3.2.0 - pip diff --git a/envs/juno_cgmlst.yaml b/envs/juno_cgmlst.yaml index 8c4d1f6..9715731 100644 --- a/envs/juno_cgmlst.yaml +++ b/envs/juno_cgmlst.yaml @@ -2,8 +2,7 @@ name: juno_cgmlst channels: - bioconda - conda-forge - - anaconda - - defaults + - nodefaults dependencies: - python=3.10.* - mamba=1.2.* @@ -26,6 +25,7 @@ dependencies: - tabulate=0.9 - biopython>=1.74 - pip=23.* + - importlib_resources 6.0.0 - pip: - "--editable=git+https://github.com/RIVM-bioinformatics/juno-library.git@v2.0.1#egg=juno_library" - types-beautifulsoup4 diff --git a/run_pipeline.sh b/run_pipeline.sh index 34631ce..e6423cd 100755 --- a/run_pipeline.sh +++ b/run_pipeline.sh @@ -44,7 +44,7 @@ export -f __conda_hashr # we can use the base installation of mamba to create the environment. # Swapping to a parent env is not necessary anymore. -mamba env create -f envs/master_env.yaml --name pipeline_env +mamba env create -f envs/juno_cgmlst.yaml --name pipeline_env conda activate pipeline_env