Project Logan assembly analysis toolkit Adapted from https://gitlab.pasteur.fr/rchikhi_pasteur/logan-analysis/
Running this system costs real
-
1_deploy_container.sh push
: Build the container defined inenv/Dockerfile
, importing reference sequence sets fromref/
. Deploy the theSteck
ECR. -
2_form_cloud.sh
: Build theSteck-batch
cloud environment using CloudFormation YAML.
run_steck.sh <runs/job_parameters.list>
: Submits a job-queue forSteck
to submit jobss.
Where dest_bucket is the name of the destination bucket, and nb_jobs is the number of jobs to submit (can't exceed 10000). The more jobs, the faster it will be. Each job takes 1 vcpu and 1.5G memory. Destination bucket file structure is decided by the task.
Tests
env/1_deploy_contiainer.sh test
: Run a local unit test of thesteck-container
env/0_run-test.sh
: Run a test of Batch jobs
Manually delete the CloudFormation stack. Also delete the ECR image.