This is the current implementation of the DNA Subway Green Line. The app catalog is implemented as Agave API applications based on Docker containers. The apps are kallisto/sleuth for quantification and differential analysis, and the Tuxedo 2 suite for novel splice sites discovery.
The repository is organized as follows: . ├── kallisto_sleuth │ ├── app-gl-ks.json │ ├── app-gl-ks-stampede2.json │ ├── docker │ │ ├── cleanup.sh │ │ ├── default_entrypoint.sh │ │ ├── Dockerfile │ │ ├── run-kallisto.sh │ │ ├── run-ks.sh │ │ ├── run-sleuth.r │ │ └── sleuth_install.r │ ├── test-ks.sh │ ├── test-ks-stampede2.sh │ ├── wrap-gl-ks.sh │ └── wrap-gl-ks-stampede2.sh ├── README.md └── tuxedo2 ├── docker │ ├── default_entrypoint.sh │ ├── Dockerfile │ ├── install-ballgown.r │ ├── run-ballgown.r │ ├── run-hisat2.sh │ ├── run-stringtie.sh │ └── run-tuxedo2.sh └── test-tuxedo2.sh
To run this workflow in some HPC environments such as Stampede2, Singularity must be used. Fortunately, it is possible to easily convert our Docker image to a Singularity one. This works with Docker version 1.6.0 or higher and Singularity 2.5.2
Start by running a local registry. We will use this registry to push the Docker image.
docker run -d -p 5000:5000 --restart=always --name registry registry:2
Then, if you haven't done so, build the Docker image.
docker build -t image_name .
Next, tag the newly built image and push it to the local registry.
docker tag image_name localhost:5000/image_name
docker push localhost:5000/image_name
If you want to test pulling the image from the local registry, you can delete image_name and localhost:5000/image_name and then pull localhost:5000/image_name from the registry.
docker pull localhost:5000/image_name
To build the Singularity image, run
SINGULARITY_NOHTTPS=true singularity build singularity_image_name.simg docker://localhost:5000/image_name
You can test the image to see if it was built successfully by running
singularity run singularity_image_name.simg
Finally, if you wish to stop the registry and remove it, run
docker container stop registry
docker container rm -v registry