Merge pull request #31 from RIVM-bioinformatics/remove_anaconda_v3

Remove anaconda in v3
RIVM-bioinformatics · Jul 19, 2023 · 9580467 · 9580467
2 parents 875a5dc + c9440f8
commit 9580467
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diff --git a/envs/juno_assembly.yaml b/envs/juno_assembly.yaml
@@ -2,8 +2,8 @@ name: juno_assembly
 channels:
   - conda-forge
   - bioconda
-  - anaconda
   - biocore
+  - nodefaults
 dependencies:
   - python=3.11.*
   - mamba=1.3.*

diff --git a/run_pipeline.sh b/run_pipeline.sh
@@ -63,13 +63,9 @@ export -f __conda_hashr
 
 
 #----------------------------------------------#
-# Create/update necessary environments
-PATH_MASTER_YAML="envs/juno_assembly.yaml"
-MASTER_NAME=$(head -n 1 ${PATH_MASTER_YAML} | cut -f2 -d ' ')
-
 # 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_assembly.yaml --name pipeline_env
 conda activate pipeline_env