create miniconda environments - delete them after execution

.ci/jenkins/executePipeline.sh

@@ -13,8 +13,8 @@ export LANG=en_US.utf-8
 #export LANG=C.UTF-8
 
 # Creation of a conda virtual environment
-# echo "=== create a conda environment ==="
-# conda create -qy -n snakemake snakemake --override-channels -c conda-forge -c bioconda
+echo "=== create a conda environment ==="
+conda create -qy -n snakemake snakemake --override-channels -c conda-forge -c bioconda
 # Activation of conda virtual environment
 echo "=== activate the conda environment ==="
 source activate snakemake
@@ -46,5 +46,5 @@ fi
 # Desactivation of the conda virtual environment
 echo "=== deactivate the conda environment ==="
 source deactivate
-# echo "=== remove conda environment ==="
-# conda env remove -qy -n snakemake
+echo "=== remove conda environment ==="
+conda env remove -qy -n snakemake

.ci/jenkins/setupConda.sh

@@ -6,16 +6,16 @@ echo "JENKINS_WORKSPACE=$1"
 ls -al ${1}
 
 # remove conda environments
-# echo "=== remove conda environments ==="
-# rm -Rf ${1}/.conda
-# rm -Rf ${1}/.condarc
-# rm -Rf ${1}/.continuum
-# rm -Rf ${1}/miniconda
+echo "=== remove conda environments ==="
+rm -Rf ${1}/.conda
+rm -Rf ${1}/.condarc
+rm -Rf ${1}/.continuum
+rm -Rf ${1}/miniconda
 
 # Download miniconda
-# wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ${1}/miniconda.sh
-# /bin/bash ${1}/miniconda.sh -b -p ${1}/miniconda
-# rm -f ${1}/miniconda.sh
+wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ${1}/miniconda.sh
+/bin/bash ${1}/miniconda.sh -b -p ${1}/miniconda
+rm -f ${1}/miniconda.sh
 
 # Setup PATH
 export PATH=${1}/miniconda/bin:$PATH