.gitpod.yml

image: gitpod/workspace-base

tasks:
- name: wget data and install mamba
  init: |
    curl -L -O https://sk13.cog.sanger.ac.uk/Coleoptera_36-way_20230217.hal
    curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
    bash Mambaforge-$(uname)-$(uname -m).sh -b -p /workspace/conda && rm Mambaforge-$(uname)-$(uname -m).sh
    /workspace/conda/bin/mamba init bash
    source ~/.bashrc

    mkdir -p /workspace/cactus_install && cd /workspace/cactus_install

    mamba create -n cactus_env -c conda-forge gxx_linux-64 hdf5 pip zlib icu lxml -y
    mamba activate  cactus_env

    git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
    cd cactus
    pip install -U .
    pip install -U -r ./toil-requirement.txt

    export LD_LIBRARY_PATH=/workspace/conda/envs/cactus_env/lib/:$LD_LIBRARY_PATH
    export C_INCLUDE_PATH=/workspace/conda/envs/cactus_env/include
    export CPLUS_INCLUDE_PATH=/workspace/conda/envs/cactus_env/include
    make -j 8

  command: |
    /workspace/conda/bin/mamba init bash
    wget https://github.com/swsnr/mdcat/releases/download/mdcat-2.0.3/mdcat-2.0.3-x86_64-unknown-linux-musl.tar.gz
    tar -zxvf mdcat-2.0.3-x86_64-unknown-linux-musl.tar.gz
    export PATH=/workspace/mdcat-2.0.3-x86_64-unknown-linux-musl/mdcat:$PATH
    rm mdcat-2.0.3-x86_64-unknown-linux-musl.tar.gz

    echo 'export LD_LIBRARY_PATH=/workspace/conda/envs/cactus_env/lib/:$LD_LIBRARY_PATH;
    export C_INCLUDE_PATH=/workspace/conda/envs/cactus_env/include;
    export CPLUS_INCLUDE_PATH=/workspace/conda/envs/cactus_env/include;
    export PATH=/workspace/cactus_install/cactus/bin:$PATH' >> ~/.bashrc
    
    source ~/.bashrc
    conda activate cactus_env
    

vscode:
  extensions:
    - anwar.papyrus-pdf

workspaceLocation: "/workspace"


github:
  prebuilds:
    # enable for the master/default branch (defaults to true)
    master: true
    # enable for all branches in this repo (defaults to false)
    branches: true
    # enable for pull requests coming from this repo (defaults to true)
    pullRequests: true
    # enable for pull requests coming from forks (defaults to false)
    pullRequestsFromForks: true
    # add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
    addComment: true
    # add a "Review in Gitpod" button to pull requests (defaults to false)
    addBadge: false
    # add a label once the prebuild is ready to pull requests (defaults to false)
    addLabel: prebuilt-in-gitpod