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.gitpod.yml
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.gitpod.yml
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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