.gitpod.yml

image: gitpod/workspace-full-vnc
# Update 7th September to reflect code base changes
ports:
  - name: JBrowseWeb
    description: The JBrowse Webserver port
    port: 3000
    onOpen: open-browser
    visibility: public

  - name: HiGlass
    description: The HiGlass port
    port: 8989
    onOpen: open-browser
    visibility: public

tasks:
  - name: Install Singularity 3.11.4
    # https://docs.sylabs.io/guides/3.0/user-guide/installation.html
    init: |
      cd /workspace/treeval-curation/

      sudo apt-get update && sudo apt-get install -y \
      build-essential \
      libssl-dev \
      uuid-dev \
      libgpgme11-dev \
      squashfs-tools \
      libseccomp-dev \
      pkg-config

      mkdir -p $GOPATH/src/github.com/sylabs && \
      cd $GOPATH/src/github.com/sylabs && \
      wget https://github.com/sylabs/singularity/releases/download/v3.11.4/singularity-ce-3.11.4.tar.gz && \
      tar -xzf singularity-ce-3.11.4.tar.gz && \
      cd ./singularity-ce-3.11.4 && \
      ./mconfig

      ./mconfig && \
      make -C ./builddir && \
      sudo make -C ./builddir install

  - name: Install Nextflow
    # https://www.nextflow.io/docs/latest/getstarted.html
    init: |
      cd /workspace/treeval-curation/

      wget -qO- https://get.nextflow.io | bash

      chmod +x nextflow

      nextflow self-update

  - name: Install JBrowse2
    # https://jbrowse.org/jb2/download/#jbrowse-cli-tools
    command: |
      cd /workspace/treeval-curation/

      npm install -g @jbrowse/cli

      jbrowse create jbrowse2

      cd jbrowse2/

      npx serve . -l 3000

  - name: Install TreeVal Pipeline
    # https://github.com/sanger-tol/treeval
    init: |
      cd /workspace/treeval-curation/

      git clone -b v1.0.0 https://github.com/sanger-tol/treeval.git

  - name: Install Curtation Pretext
    # https://github.com/sanger-tol/curationpretext
    init: |
      cd /workspace/treeval-curation/

      git clone -b dev https://github.com/sanger-tol/curationpretext.git

  - name: Install HiGlass
    # https://docs.higlass.io/tutorial.html
    init: |
      cd /workspace/treeval-curation/

      pip install higlass-manage

      higlass-manage start

  - name: Alias Nextflow
    init: |
      cd /workspace/treeval-curation/

      echo "alias nextflow_cmd='/workspace/treeval-curation/nextflow'" >> ~/.bashrc

      source ~/.bashrc

  - name: Download busco for nematode
    init: |
      cd /workspace/treeval-curation/

      curl https://dp24.cog.sanger.ac.uk/Busco.tar.gz | tar xzf -

  - name: Download Nematode Test data and make synteny
    init: |
      cd /workspace/treeval-curation/

      curl https://dp24.cog.sanger.ac.uk/Nematode.tar.gz | tar xzf -

      mkdir -p /workspace/treeval-curation/synteny/nematode/

      cp /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa /workspace/treeval-curation/synteny/nematode/SuperNematode.fa

  - name: Download Lepidoptera data
    init: |
      cd /workspace/treeval-curation/

      curl https://dp24.cog.sanger.ac.uk/ilTorViri5.tar.gz | tar xzf -

  - name: Download Genomic Alignment data
    init: |
      cd /workspace/treeval-curation/

      curl https://dp24.cog.sanger.ac.uk/AlignmentData.tar.gz | tar xzf -

  - name: Open Tutorial Page
    init: |
      gp preview https://bga23.org/treeval-curation/Tutorial/

github:
  prebuilds:
    # enable for the master/default branch (defaults to true)
    master: 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: true
    # add a label once the prebuild is ready to pull requests (defaults to false)
    addLabel: prebuilt-in-gitpod

vscode:
  extensions: # based on nf-core.nf-core-extensionpack
    - codezombiech.gitignore # Language support for .gitignore files
    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
    - nextflow.nextflow # Nextflow syntax highlighting
    - oderwat.indent-rainbow # Highlight indentation level
    - streetsidesoftware.code-spell-checker # Spelling checker for source code