docker-phyloseq

Updates

• Point shiny::runGitHub to a fork (https://github.com/paulzierep/shiny-phyloseq) where BiocManager is only installed if required. Thus starting the app without installations (since all packages are installed in the container) which should allow galaxy to run the app.

Test image locally

docker build . -t 'shiny-phyloseq'
docker run -p 3838:3838 shiny-phyloseq
docker run -v /home/paul/git/my-repositories/shiny-phyloseq/data:/shiny_input -p 3838:3838 shiny-phyloseq #with the hacked galaxy input

Uplodad

• Create a release in github
• The CI will push it to quay.io

Test with:

docker pull quay.io/paulzierep/shinyphyloseq:0.1

Access on http://127.0.0.1:3838/

Ideas

• just run shiny::runGitHub; then kill it with timeout (https://stackoverflow.com/questions/48740277/error-using-timeout-command-invalid-time-interval)

Links

• the tool wrapper: usegalaxy-eu/galaxy#233
• the tool fork: https://github.com/paulzierep/shiny-phyloseq

Wrapper

Test wrapper locally

Get Galaxy !

GALAXY_PATH=~/git/galaxy # modify
mv $GALAXY_PATH/config/galaxy.yml.interactivetools $GALAXY_PATH/config/galaxy.yml
mv $GALAXY_PATH/config/job_conf.yml.interactivetools $GALAXY_PATH/config/job_conf.yml
mv $GALAXY_PATH/config/tool_conf.xml.sample $GALAXY_PATH/config/tool_conf.xml #add interactive tools