INNER CODE UNIT · Python

envcheck3

franciscozorrilla/metaGEM · workflow/metaGEM.sh:131

envcheck3=$(conda info --envs|grep -w prokkaroary|wc -l)
if [[ "$envcheck3" -ge 1 ]]; then
    echo -e "detected!\n"
else
    echo -e "not detected, please run the env_setup.sh script!\n"
fi

# run createFolders rule to create folders in case any of them are missing
echo -e "Checking folders in workspace $pwd ... "
nFolders=$(ls -d */|wc -l)
if [[ "$nFolders" -le 20 ]]; then
    while true; do
        read -p "Some folders appear to be missing, do you wish to run the createFolders Snakefile rule? (y/n)" yn
        case $yn in
            [Yy]* ) echo "Running the createFolders snakefile rule ... " && snakemake createFolders -j1; break;;
            [Nn]* ) echo "Skipping folder creation ... "; break;;
            * ) echo "Please answer yes or no.";;
        esac

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