WIP,...

Author: aerijman

run_test.sh

@@ -12,8 +12,10 @@ tmp="${pwd}/test_data/tmp"
 if command -v conda &> /dev/null; then
     activate_conda=$(type -a conda | grep -Eo '/.*conda' | head -n 1 | sed 's/\/bin\|\/condabin.*$/\/bin\/activate/')
 else
-    echo "please install conda. Then run this script"   
+    echo "please install conda. Then run this script"
+    exit 1
 fi
+conda init
 . ${activate_conda} || echo "Perhaps conda is not in: $(type -a conda) ?"
 
 # All these are to avoid dependencies problems... # 
@@ -23,7 +25,6 @@ conda config --add channels defaults
 conda config --add channels conda-forge
 conda config --add channels bioconda
 conda install -c conda-forge libgcc-ng=12
-conda init
 # 
 
 conda create --name nextflow.emseq --yes python=3.8 && conda install --name nextflow.emseq --yes bioconda:nextflow=23.10 bioconda::samtools=1.19