.gitpod.yml

image: gitpod/workspace-base
# image: condaforge/mambaforge:24.7.1-0

tasks:
- name: install mamba
  init: |
    cd /workspace
    wget "https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-24.3.0-0-Linux-x86_64.sh"
    bash Mambaforge-24.3.0-0-Linux-x86_64.sh -b -p /workspace/mambaforge && rm Mambaforge-24.3.0-0-Linux-x86_64.sh

    /workspace/mambaforge/bin/mamba init bash
    source ${HOME}/.bashrc
    mamba create -n smudgeplot -c conda-forge r-base r-argparse r-viridis -y
    mamba activate smudgeplot
    pip3 install numpy pandas

    cd /workspace
    mkdir src bin && cd src # create directories for source code & binaries
    git clone -b sploidyplot https://github.com/KamilSJaron/smudgeplot
    git clone https://github.com/thegenemyers/FastK

    cd smudgeplot
    make -s INSTALL_PREFIX=/workspace
    cd ../FastK && make
    install -c FastK Fastrm Fastmv Fastcp Fastmerge Histex Tabex Profex Logex Vennex Symmex Haplex Homex Fastcat /workspace/bin/

    cd /workspace
    mkdir -p smudgeplot/data/Scer && wget -P smudgeplot/data/Scer https://sk13.cog.sanger.ac.uk/SRR3265401_{1,2}.fastq.gz
    
    gp sync-done bundle
    
- name: activate mamba
  init: gp sync-await bundle # Wait for previous 'inits' to complete
  command: |
    cd /workspace
    /workspace/mambaforge/bin/mamba init bash
    source ~/.bashrc 
    mamba activate smudgeplot
    
    export PATH=/workspace/bin:"$PATH"

vscode:
  extensions:
    - anwar.papyrus-pdf

workspaceLocation: "/workspace"