.gitpod.yml

image: gitpod/workspace-base

tasks:
- name: install gfastats
  command: |
    cd /workspace
    #gfastats
    wget https://github.com/vgl-hub/gfastats/releases/download/v1.3.7/gfastats.v1.3.7-linux.zip
    unzip gfastats.v1.3.7-linux.zip
    chmod a+x ./gfastats
    #rdeval
    wget https://github.com/vgl-hub/rdeval/releases/download/v0.0.1/rdeval.v0.0.1-linux.zip
    unzip rdeval.v0.0.1-linux.zip
    chmod a+x ./rdeval
    #kreeq
    wget https://github.com/vgl-hub/kreeq/releases/download/v0.0.1/kreeq.v0.0.1-linux.zip
    unzip kreeq.v0.0.1-linux.zip
    chmod a+x ./kreeq
    export PATH=/workspace:$PATH
    #large data
    wget https://genomeark.s3.amazonaws.com/trainingmaterials/BGA2023/large_input.fasta.gz
    wget https://genomeark.s3.amazonaws.com/trainingmaterials/BGA2023/filtered.fastq
    wget https://genomeark.s3.amazonaws.com/trainingmaterials/BGA2023/filtered2.fastq
    wget https://genomeark.s3.amazonaws.com/trainingmaterials/BGA2023/input.fa

workspaceLocation: "/workspace"