added mamba to env

metagenlab · May 11, 2021 · c839fd1 · c839fd1
1 parent 5889411
commit c839fd1
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diff --git a/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@ RUN conda config --add channels conda-forge && \
 	conda config --add channels default
 
 # download and install covpipe
-RUN git clone https://github.com/metagenlab/GENCOV.git && echo OK9
+RUN git clone https://github.com/metagenlab/GENCOV.git && echo OK10
 WORKDIR /GENCOV
 RUN bash ncov_minipipe.conda.setup/setup_env.sh && /GENCOV/covpipe_environment/bin/snakemake -s /GENCOV/ncov_minipipe.snake --cores 16 --use-conda --conda-prefix /GENCOV/.snakemake/conda --configfile /GENCOV/ncov_minipipe.config --conda-create-envs-only  &&  conda clean -a
 

diff --git a/ncov_minipipe.conda.setup/setup_env.sh b/ncov_minipipe.conda.setup/setup_env.sh
@@ -41,6 +41,7 @@ update_conda_or_install(){
         -c conda-forge  -c bioconda -c defaults \
         "python>=3.6.0" \
         "snakemake>=5.26" \
+        "mamba" \
         strictyaml \
         -ymp "${ENVPATH}"
 }