Snakemake and singularity

[diegovevo]

Attempting to run a Snakemake workflow that uses a Singularity container

Steps to Reproduce

Run a Snakemake workflow that uses the "container:" directive w/ the --use-singularity engine flag (as defined in MANIFEST.json)

Relevant Logs

Tue, 18 Oct 2022 23:44:17 -0400 == Running Workflow ==
Tue, 18 Oct 2022 23:44:17 -0400 snakemake --aws-batch --cores all --aws-batch-workflow-role arn:aws:iam::310073513818:role/Agc-Context-vevosnakemake-snakemakeHeadBatchBatchR-1FKMRWHKYR425 --aws-batch-task-queue arn:aws:batch:us-east-2:310073513818:job-queue/snakemakeTaskBatchJobQue-w2O91KJuH1mD7RGl --aws-batch-fsap-id fsap-0615c02628b8d7e34 -j 2 --forceall --use-conda --use-singularity --aws-batch-tags AWS_BATCH_PARENT_JOB_ID=abc4889f-2ed1-4981-a970-206868f7f17b --aws-batch-efs-project-path=snakemake/abc4889f-2ed1-4981-a970-206868f7f17b --latency-wait 60
Tue, 18 Oct 2022 23:44:17 -0400 SNAKEMAKE pid: 27
Tue, 18 Oct 2022 23:44:17 -0400 [1]+  Running                 $ENGINE_RUN_CMD $ENGINE_PARAMS 2>&1 &
Tue, 18 Oct 2022 23:44:17 -0400 waiting ..
Tue, 18 Oct 2022 23:44:18 -0400 Building DAG of jobs...
Tue, 18 Oct 2022 23:44:20 -0400 WorkflowError:
Tue, 18 Oct 2022 23:44:20 -0400 The singularity command has to be available in order to use singularity integration.
Tue, 18 Oct 2022 23:44:20 -0400 === Running Cleanup ===
Tue, 18 Oct 2022 23:44:20 -0400 === Bye! ===

Expected Behavior

Expecting singularity to be installed and set up in the AMI that is being used for AGC

Actual Behavior

Singularity not installed

Operating System: Ubuntu
AGC Version: 1.5.1

[johnnyvevo]

really need this AWS!!