refactor: rename master environment file in runpipeline.sh script

RIVM-bioinformatics · Jul 18, 2023 · bf08695 · bf08695
1 parent 007826b
commit bf08695
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diff --git a/envs/juno_cgmlst.yaml b/envs/juno_cgmlst.yaml
@@ -25,6 +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