comparison install_amplicon_analysis-1.3.5.sh @ 44:213b5cdecb70 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit a0f1569b4882ca4f9cee613615fe75771bbf0b23-dirty

43:496cc0ddce3d

    echo ""
    echo -n "Rewriting conda shebangs..."
    rewrite_conda_shebangs
    echo "ok"
    echo -n "Adding conda bin to PATH..."
    PATH=${CONDA_BIN}:$PATH
    echo "ok"
    cd $cwd
    rm -rf $wd/*
    rmdir $wd
}

  - r-tidyverse=1.2.1
  - bioconductor-dada2=1.8
  - bioconductor-biomformat=1.8.0
EOF
    ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
    echo Created conda environment in ${ENV_DIR}
    cd $cwd
    rm -rf $wd/*
    rmdir $wd
    #

44:213b5cdecb70

    echo ""
    echo -n "Rewriting conda shebangs..."
    rewrite_conda_shebangs
    echo "ok"
    echo -n "Adding conda bin to PATH..."
    export PATH=${CONDA_BIN}:$PATH
    echo "ok"
    cd $cwd
    rm -rf $wd/*
    rmdir $wd
}

  - r-tidyverse=1.2.1
  - bioconductor-dada2=1.8
  - bioconductor-biomformat=1.8.0
EOF
    ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
    if [ $? -ne 0 ] ; then
	fail "Non-zero exit status from 'conda env create'"
    elif [ ! -e "${ENV_DIR}" ] ; then
	fail "Failed to create conda environment: ${ENV_DIR} not found"
    fi
    echo Created conda environment in ${ENV_DIR}
    cd $cwd
    rm -rf $wd/*
    rmdir $wd
    #