mwvaughn/fastqc-application

fastqc-application

0. Contents

.
├── Dockerfile
├── README.md
├── app.ini
└── fastqc-0.11.7
    ├── _util
    │   ├── VERSION
    │   └── container_exec.sh
    ├── app.json.j2
    ├── job.json.j2
    ├── runner-template.sh
    └── tester.sh

1. Clone

git clone https://github.com/wjallen/fastqc-application
cd fastqc-application/

2. Personalize

./app.ini

=> change to your docker username / preferred repo and tag

./fastqc-0.11.7/app.json.j2

=> change executionSystem, deploymentSystem, and deploymentPath if necessary

./fastqc-0.11.7/runner-template.sh

=> change CONTAINER_IMAGE to your preferred repo source

3. Deploy

apps-deploy -E app.ini -f Dockerfile -a fastqc-0.11.7/app.json.j2 -j fastqc-0.11.7/job.json.j2 -T ./

4. Test

jobs-submit -F deploy-username-job.json
jobs-output-list <jobid>

=> job was a success if read1_fastqc.html exists