use mamba to build conda envs

metagenlab · Oct 13, 2023 · 30bbb75 · 30bbb75
1 parent 2e3f53c
commit 30bbb75
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/bin/zdb b/bin/zdb
@@ -351,7 +351,7 @@ elif [[ "$1" == "webapp" ]]; then
 		conda_prefix="$NEXTFLOW_DIR/conda-env/webapp"
 		if [[ ! -e "$conda_prefix" ]]; then
 			echo "Building conda environment..."
-			conda env create --prefix $conda_prefix -f $NEXTFLOW_DIR/conda/webapp.yaml &> conda_log
+			mamba env create --prefix $conda_prefix -f $NEXTFLOW_DIR/conda/webapp.yaml &> conda_log
 			if [[ $? -eq 0 ]]; then
 				echo "Done"
 			else

diff --git a/nextflow.config b/nextflow.config
@@ -60,6 +60,7 @@ singularity.autoMounts = true
 
 docker.enabled = "$params.docker" == "true"?true:false
 conda.enabled = "$params.conda" == "true"?true:false
+conda.useMamba = true
 
 params.annotation_container = "registry.hub.docker.com/metagenlab/annotation-pipeline:1.3.1"