merge remove anaconda branch

RIVM-bioinformatics · Jul 18, 2023 · 183b63a · 183b63a
2 parents e26ca85 + bf08695
commit 183b63a
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git 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
@@ -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/[email protected]#egg=juno_library"
     - types-beautifulsoup4

diff --git 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