This repository contains tools which JACS runs on the cluster to process data.
Each sub directory contains a single tool which can be built into a Singularity container.
For information on how to create a new tool, read about Contributing.
To build one or more tools:
./manage.sh build [tool1] [tool2] [tool3] ...
This creates a set of corresponding img files in the build directory which can be run with Singularity.
To open a shell into a built container:
./manage.sh shell [tool]
Regression tests can be added to each container under the "test" directory. Each sub-directory in the "tests" directory is considered to be a standalone test. A file called test.sh must be placed in each test directory. To run tests:
./manage test [tool1] [tool2] [tool3] ...
To deploy a built container to another location, you must first define the target location in your environment, e.g. in your ~/.bashrc file:
export JACS_SINGULARITY_DIR=/groups/jacs/jacsDev/servers/jacs-data/executables/singularity
Then
./manage.sh deploy [tool1] [tool2] [tool3] ...
You can delete existing builds for one or more containers with the clean command:
./manage.sh clean [tool1] [tool2] [tool3] ...
Container versioning is done in the Singularity build file. When making changes to a container, make sure to increment the VERSION variable in the Singularity file before building or deploying that container.
To use container named <container.img> which contains an app called you can invoke Singularity as follows.
B1=/external/path1
B2=/external/path2
singularity run -B $B1 -B $B2 --app appName container.img -i $B1 -o $B2
All external paths which the container needs to access must be mounted with -B flags.