Test instructions

docker-compose

git clone https://github.com/denis-yuen/compose_tutorial.git
cd compose_tutorial/
tmux
docker-compose up
<new terminal>
curl http://0.0.0.0:5000/
<in original terminal>
<ctrl -c>
git checkout mount_example
docker-compose up
<second terminal>
curl http://0.0.0.0:5000/
<edit app.py>
curl http://0.0.0.0:5000/

history

sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update && sudo apt-get install -y oracle-java8-set-default
mkdir -p ~/bin
curl -L -o ~/bin/dockstore https://github.com/ga4gh/dockstore/releases/download/1.5.1/dockstore
chmod +x ~/bin/dockstore
echo 'export PATH=~/bin:$PATH' >> ~/.bashrc
source ~/.bashrc
mkdir -p ~/.dockstore
printf "token: fobar\nserver-url: https://dockstore.org:443/api\n" > ~/.dockstore/config
sudo apt install python-pip
curl -o requirements.txt "https://dockstore.org:443/api/metadata/runner_dependencies?client_version=1.5.1&python_version=2"
pip install -r requirements.txt
curl -sSL https://get.docker.com/ | sh
sudo usermod -aG docker ubuntu
# exit (and then re-enter)
docker --version
java -version
dockstore --version

running a workflow in CWL

git clone https://github.com/CancerCollaboratory/dockstore-tool-bamstats.git
cd dockstore-tool-bamstats/
dockstore tool launch --local-entry Dockstore.cwl --json test.json

running a workflow in WDL

git clone https://github.com/CancerCollaboratory/dockstore-tool-bamstats.git
cd dockstore-tool-bamstats/
dockstore tool launch --local-entry Dockstore.wdl --json test.wdl.json

Useful Docker commands

git clone https://github.com/CancerCollaboratory/dockstore-tool-bamstats.git
cd dockstore-tool-bamstats/

docker build -t foo .
grep "dockerPull" Dockstore.cwl
docker build -t quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 .
docker run -ti quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 /bin/bash
java -jar /opt/BAMStats-1.25/BAMStats-1.25.jar --help