.gitpod.yml

image:
  file: .gitpod.Dockerfile

tasks:
  - name: Setup For BwoB Intro To Bioinformatics (Conda, QIIME 2, q2-krona, and Krona)
    init: |
      CONDA_DIR="/workspace/miniconda3"
      if [ ! -d "$CONDA_DIR" ]; then
        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
        bash Miniconda3-latest-Linux-x86_64.sh -b -p $CONDA_DIR
        rm Miniconda3-latest-Linux-x86_64.sh
      fi
      echo 'export PATH="$CONDA_DIR/bin:$PATH"' >> $HOME/.bashrc
      echo '. $CONDA_DIR/etc/profile.d/conda.sh' >> $HOME/.bashrc
      source $HOME/.bashrc
      conda init bash
      if [ ! -d "$CONDA_DIR/envs/qiime2-amplicon-2024.5" ]; then
        conda update -n base -c defaults conda
        max_retries=3
        retry_count=0
        while [ $retry_count -lt $max_retries ]; do
          if conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml; then
            echo "QIIME 2 environment created successfully"
            break
          else
            echo "Failed to create QIIME 2 environment. Retrying in 10 seconds..."
            sleep 10
            ((retry_count++))
          fi
        done
        if [ $retry_count -eq $max_retries ]; then
          echo "Failed to create QIIME 2 environment after $max_retries attempts"
        fi
      fi
      source $HOME/.bashrc
      conda activate qiime2-amplicon-2024.5
      conda install -c bioconda krona -y
      ktUpdateTaxonomy.sh
      pip install git+https://github.com/kaanb93/q2-krona.git
      qiime dev refresh-cache
    command: |
      source $HOME/.bashrc
      conda activate qiime2-amplicon-2024.5
      echo 'conda activate qiime2-amplicon-2024.5' >> $HOME/.bashrc
      echo "Conda, QIIME 2, q2-krona, and Krona setup complete. Verifying installation..."
      conda info
      qiime --version
      echo "Verifying Krona installation:"
      which ktImportText
      echo "Verifying q2-krona plugin installation:"
      qiime krona --help
      echo "Setup complete. You can now use QIIME 2 commands including the q2-krona plugin."

vscode:
  extensions:
    - ms-python.python
    - ms-python.debugpy