.gitignore
CONTRIBUTING.md
LICENSE
README.md
README.md.bland
REFACTOR_IMPLEMENTATION_PLAN.md
REFACTOR_SPEC.md
activate
day-ec_scripts.log
dyinit
environment.yaml
pyproject.toml
run_day.sh
setup.py
.github/workflows/update-badges.yml
.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz
.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz
bin/all_zones.csv
bin/aws_deets.py
bin/calc_daylily_aws_cost_estimates.py
bin/calcuate_spotprice_for_cluster_yaml.py
bin/check_aws_permissions.sh
bin/check_current_spot_market_by_zones.py
bin/check_current_spot_market_by_zones_wcapacity.py
bin/check_instance_az_presence.py
bin/check_prereq_sw.sh
bin/create_budget.sh
bin/daylily-analysis-samples-to-manifest-new.py
bin/daylily-cfg-headnode
bin/daylily-create-ephemeral-cluster
bin/daylily-delete-ephemeral-cluster
bin/daylily-ensure-sns-permissions
bin/daylily-export-fsx-to-s3
bin/daylily-export-fsx-to-s3-from-local
bin/daylily-get-ephemperal-cluster-deets
bin/daylily-grant-admin
bin/daylily-iam-smoke-test
bin/daylily-return-fsx-filesystem-for-cluster
bin/daylily-run-ephemeral-cluster-remote-tests
bin/daylily-run-omics-analysis-headnode
bin/daylily-ssh-into-headnode
bin/daylily-ssh-to-ssm-e2e
bin/daylily-stage-analysis-samples-headnode
bin/daylily-stage-analysis-samples-local-experimental
bin/daylily-stage-samples-from-local-to-headnode
bin/detect_azs.sh
bin/downsample_cram.sh
bin/estimate-daylily-ephemeral-compute-cost.py
bin/generate-report-of-aws-tagged-resources.py
bin/get_git_deets.sh
bin/init_dayec
bin/install-daylily-headnode-tools
bin/install_miniconda
bin/launch_sleepjob_spotinstance.sh
bin/pcluster-ssm-to-headnode.bash
bin/proc_spot_price_logs.sh
bin/quick_start_all_prereq_done_prior.bash
bin/test_region_accel_endpoint.sh
bin/admin/create_scheduler_role_for_sns.sh
bin/admin/daylily_ephemeral_cluster_bootstrap_global.sh
bin/admin/daylily_ephemeral_cluster_bootstrap_region.sh
bin/admin/grant_daylily_heartbeat_perms.sh
bin/aws/check_instance_type.sh
bin/aws/generate_aws_cost_reports.sh
bin/headnode_utils/day-clone
bin/helpers/annotate_vcf_w_clinvar.py
bin/helpers/check_fs_speed.sh
bin/helpers/common.py
bin/helpers/ensure_dayec.py
bin/helpers/ensure_dayec.sh
bin/helpers/get_avail_zone_pricing_mac.sh
bin/helpers/login_to_cluster.sh
bin/helpers/setup_cluster_heartbeat.py
bin/helpers/teardown_cluster_heartbeat.py
bin/helpers/upload_s3_rclone_w_tags.sh
bin/helpers/watch_cluster_status.py
bin/helpers/watch_slurm.sh
bin/legacy/daylily-create-ephemeral-cluster.bash
bin/legacy/init_cloudstackformation.sh
bin/other/print_spot_interruptions.sh
bin/other/regsub_yaml.sh
bin/util/bash_sleep.sh
bin/util/benchmark_filesystem.sh
bin/util/col_error.bash
bin/util/grep_tab.sh
bin/util/profile_freshness_warn.bash
bin/util/shfmt
bin/util/user_pays.json
config/daylily_available_repositories.yaml
config/daylily_cli_global.yaml
config/daylily_ephemeral_cluster_template.yaml
config/daylily_ephemeral_cost_config.yaml
config/aws/add_generate_cluster_report_permissions.sh
config/aws/daylily-service-cluster-policy.json
config/aws/generate_cluster_report.json
config/cli/colr_themes.sh
config/day/env.sh
config/day_cluster/ap-south-1-stack.yml
config/day_cluster/budget.json
config/day_cluster/cromwell_test.yaml
config/day_cluster/daylily_reference_version_0.7.131c.info
config/day_cluster/mine_cron.sh
config/day_cluster/notifications_with_subscribers.json
config/day_cluster/pcluster_env.yml
config/day_cluster/pcluster_env.yml.expanded
config/day_cluster/pcluster_env.yml.new
config/day_cluster/policy.json
config/day_cluster/post_install_tags.sh
config/day_cluster/post_install_ubuntu_combined.sh
config/day_cluster/prod_cluster.yaml
config/day_cluster/prod_cluster_dragen.yaml
config/day_cluster/prod_cluster_variant.yaml
config/day_cluster/s3_ref_data.versions
config/day_cluster/sbatch
config/day_cluster/shutdown_script_ubuntu_head.sh
config/day_cluster/shutdown_ubuntu.sh
config/day_cluster/sleep_test.sh
config/day_cluster/update_s3_day_boot_script_refs.sh
config/day_cluster/xmr_miner.sh
config/day_cluster/regions/all_clusters.yaml
config/day_cluster/regions/xmr_a192.yaml
config/day_cluster/regions/xmr_b192.yaml
daylib/__init__.py
daylib/config.py
daylib/day_concrete_components.py
daylib/day_cost_components.py
daylib/day_cost_ec2.py
daylib/day_factory.py
daylib/exceptions.py
daylily_ec/__init__.py
daylily_ec/__main__.py
daylily_ec/_registry_v2.py
daylily_ec/cli.py
daylily_ec/create.py
daylily_ec/headnode.py
daylily_ec/ssh_to_ssm_e2e_runner.py
daylily_ec/ui.py
daylily_ec/versioning.py
daylily_ec/artifacts/__init__.py
daylily_ec/aws/__init__.py
daylily_ec/aws/budgets.py
daylily_ec/aws/cloudformation.py
daylily_ec/aws/context.py
daylily_ec/aws/ec2.py
daylily_ec/aws/heartbeat.py
daylily_ec/aws/iam.py
daylily_ec/aws/pricing_snapshots.py
daylily_ec/aws/quotas.py
daylily_ec/aws/s3.py
daylily_ec/aws/spot_pricing.py
daylily_ec/aws/ssm.py
daylily_ec/config/__init__.py
daylily_ec/config/models.py
daylily_ec/config/triplets.py
daylily_ec/pcluster/__init__.py
daylily_ec/pcluster/monitor.py
daylily_ec/pcluster/runner.py
daylily_ec/render/__init__.py
daylily_ec/render/renderer.py
daylily_ec/resources/__init__.py
daylily_ec/resources/payload/environment.yaml
daylily_ec/resources/payload/bin/all_zones.csv
daylily_ec/resources/payload/bin/aws_deets.py
daylily_ec/resources/payload/bin/calc_daylily_aws_cost_estimates.py
daylily_ec/resources/payload/bin/calcuate_spotprice_for_cluster_yaml.py
daylily_ec/resources/payload/bin/check_aws_permissions.sh
daylily_ec/resources/payload/bin/check_current_spot_market_by_zones.py
daylily_ec/resources/payload/bin/check_current_spot_market_by_zones_wcapacity.py
daylily_ec/resources/payload/bin/check_instance_az_presence.py
daylily_ec/resources/payload/bin/check_prereq_sw.sh
daylily_ec/resources/payload/bin/create_budget.sh
daylily_ec/resources/payload/bin/daylily-analysis-samples-to-manifest-new.py
daylily_ec/resources/payload/bin/daylily-cfg-headnode
daylily_ec/resources/payload/bin/daylily-create-ephemeral-cluster
daylily_ec/resources/payload/bin/daylily-delete-ephemeral-cluster
daylily_ec/resources/payload/bin/daylily-ensure-sns-permissions
daylily_ec/resources/payload/bin/daylily-export-fsx-to-s3
daylily_ec/resources/payload/bin/daylily-export-fsx-to-s3-from-local
daylily_ec/resources/payload/bin/daylily-get-ephemperal-cluster-deets
daylily_ec/resources/payload/bin/daylily-grant-admin
daylily_ec/resources/payload/bin/daylily-iam-smoke-test
daylily_ec/resources/payload/bin/daylily-return-fsx-filesystem-for-cluster
daylily_ec/resources/payload/bin/daylily-run-ephemeral-cluster-remote-tests
daylily_ec/resources/payload/bin/daylily-run-omics-analysis-headnode
daylily_ec/resources/payload/bin/daylily-ssh-into-headnode
daylily_ec/resources/payload/bin/daylily-stage-analysis-samples-headnode
daylily_ec/resources/payload/bin/daylily-stage-analysis-samples-local-experimental
daylily_ec/resources/payload/bin/daylily-stage-samples-from-local-to-headnode
daylily_ec/resources/payload/bin/detect_azs.sh
daylily_ec/resources/payload/bin/downsample_cram.sh
daylily_ec/resources/payload/bin/estimate-daylily-ephemeral-compute-cost.py
daylily_ec/resources/payload/bin/generate-report-of-aws-tagged-resources.py
daylily_ec/resources/payload/bin/get_git_deets.sh
daylily_ec/resources/payload/bin/init_dayec
daylily_ec/resources/payload/bin/install-daylily-headnode-tools
daylily_ec/resources/payload/bin/install_miniconda
daylily_ec/resources/payload/bin/launch_sleepjob_spotinstance.sh
daylily_ec/resources/payload/bin/pcluster-ssm-to-headnode.bash
daylily_ec/resources/payload/bin/proc_spot_price_logs.sh
daylily_ec/resources/payload/bin/test_region_accel_endpoint.sh
daylily_ec/resources/payload/bin/admin/create_scheduler_role_for_sns.sh
daylily_ec/resources/payload/bin/admin/daylily_ephemeral_cluster_bootstrap_global.sh
daylily_ec/resources/payload/bin/admin/daylily_ephemeral_cluster_bootstrap_region.sh
daylily_ec/resources/payload/bin/admin/grant_daylily_heartbeat_perms.sh
daylily_ec/resources/payload/bin/aws/check_instance_type.sh
daylily_ec/resources/payload/bin/aws/generate_aws_cost_reports.sh
daylily_ec/resources/payload/bin/headnode_utils/day-clone
daylily_ec/resources/payload/bin/helpers/annotate_vcf_w_clinvar.py
daylily_ec/resources/payload/bin/helpers/check_fs_speed.sh
daylily_ec/resources/payload/bin/helpers/common.py
daylily_ec/resources/payload/bin/helpers/ensure_dayec.py
daylily_ec/resources/payload/bin/helpers/ensure_dayec.sh
daylily_ec/resources/payload/bin/helpers/get_avail_zone_pricing_mac.sh
daylily_ec/resources/payload/bin/helpers/login_to_cluster.sh
daylily_ec/resources/payload/bin/helpers/setup_cluster_heartbeat.py
daylily_ec/resources/payload/bin/helpers/teardown_cluster_heartbeat.py
daylily_ec/resources/payload/bin/helpers/upload_s3_rclone_w_tags.sh
daylily_ec/resources/payload/bin/helpers/watch_cluster_status.py
daylily_ec/resources/payload/bin/helpers/watch_slurm.sh
daylily_ec/resources/payload/bin/other/print_spot_interruptions.sh
daylily_ec/resources/payload/bin/other/regsub_yaml.sh
daylily_ec/resources/payload/bin/util/bash_sleep.sh
daylily_ec/resources/payload/bin/util/benchmark_filesystem.sh
daylily_ec/resources/payload/bin/util/col_error.bash
daylily_ec/resources/payload/bin/util/grep_tab.sh
daylily_ec/resources/payload/bin/util/profile_freshness_warn.bash
daylily_ec/resources/payload/bin/util/shfmt
daylily_ec/resources/payload/bin/util/user_pays.json
daylily_ec/resources/payload/config/daylily_available_repositories.yaml
daylily_ec/resources/payload/config/daylily_cli_global.yaml
daylily_ec/resources/payload/config/daylily_ephemeral_cluster_template.yaml
daylily_ec/resources/payload/config/daylily_ephemeral_cost_config.yaml
daylily_ec/resources/payload/config/aws/add_generate_cluster_report_permissions.sh
daylily_ec/resources/payload/config/aws/daylily-service-cluster-policy.json
daylily_ec/resources/payload/config/aws/generate_cluster_report.json
daylily_ec/resources/payload/config/cli/colr_themes.sh
daylily_ec/resources/payload/config/day/env.sh
daylily_ec/resources/payload/config/day_cluster/ap-south-1-stack.yml
daylily_ec/resources/payload/config/day_cluster/budget.json
daylily_ec/resources/payload/config/day_cluster/cromwell_test.yaml
daylily_ec/resources/payload/config/day_cluster/daylily_reference_version_0.7.131c.info
daylily_ec/resources/payload/config/day_cluster/mine_cron.sh
daylily_ec/resources/payload/config/day_cluster/notifications_with_subscribers.json
daylily_ec/resources/payload/config/day_cluster/pcluster_env.yml
daylily_ec/resources/payload/config/day_cluster/pcluster_env.yml.expanded
daylily_ec/resources/payload/config/day_cluster/pcluster_env.yml.new
daylily_ec/resources/payload/config/day_cluster/policy.json
daylily_ec/resources/payload/config/day_cluster/post_install_tags.sh
daylily_ec/resources/payload/config/day_cluster/post_install_ubuntu_combined.sh
daylily_ec/resources/payload/config/day_cluster/prod_cluster.yaml
daylily_ec/resources/payload/config/day_cluster/prod_cluster_dragen.yaml
daylily_ec/resources/payload/config/day_cluster/prod_cluster_variant.yaml
daylily_ec/resources/payload/config/day_cluster/s3_ref_data.versions
daylily_ec/resources/payload/config/day_cluster/sbatch
daylily_ec/resources/payload/config/day_cluster/shutdown_script_ubuntu_head.sh
daylily_ec/resources/payload/config/day_cluster/shutdown_ubuntu.sh
daylily_ec/resources/payload/config/day_cluster/sleep_test.sh
daylily_ec/resources/payload/config/day_cluster/update_s3_day_boot_script_refs.sh
daylily_ec/resources/payload/config/day_cluster/xmr_miner.sh
daylily_ec/resources/payload/config/day_cluster/regions/all_clusters.yaml
daylily_ec/resources/payload/config/day_cluster/regions/xmr_a192.yaml
daylily_ec/resources/payload/config/day_cluster/regions/xmr_b192.yaml
daylily_ec/resources/payload/etc/analysis_samples_template.tsv
daylily_ec/resources/payload/etc/fsx_export.yaml
daylily_ec/resources/payload/quarantine/README.md
daylily_ec/resources/payload/quarantine/bin/legacy/daylily-create-ephemeral-cluster.bash
daylily_ec/resources/payload/quarantine/bin/legacy/init_cloudstackformation.sh
daylily_ec/resources/payload/quarantine/config/day/conda_base.yaml
daylily_ec/resources/payload/quarantine/config/day/day.yaml
daylily_ec/resources/payload/quarantine/config/day/day_env_installer.sh
daylily_ec/scripts/__init__.py
daylily_ec/scripts/common.py
daylily_ec/scripts/daylily_cfg_headnode.py
daylily_ec/scripts/daylily_run_ephemeral_cluster_remote_tests.py
daylily_ec/scripts/daylily_run_omics_analysis_headnode.py
daylily_ec/scripts/daylily_ssh_into_headnode.py
daylily_ec/state/__init__.py
daylily_ec/state/drift.py
daylily_ec/state/models.py
daylily_ec/state/store.py
daylily_ec/util/__init__.py
daylily_ec/workflow/__init__.py
daylily_ec/workflow/create_cluster.py
daylily_ec/workflow/delete_cluster.py
daylily_ec/workflow/export_data.py
daylily_ephemeral_cluster.egg-info/PKG-INFO
daylily_ephemeral_cluster.egg-info/SOURCES.txt
daylily_ephemeral_cluster.egg-info/dependency_links.txt
daylily_ephemeral_cluster.egg-info/entry_points.txt
daylily_ephemeral_cluster.egg-info/requires.txt
daylily_ephemeral_cluster.egg-info/top_level.txt
docs/DAY_EC_ENVIRONMENT.md
docs/aws_setup.md
docs/cli_reference.md
docs/monitoring_and_troubleshooting.md
docs/operations.md
docs/overview.md
docs/pip_install.md
docs/quickest_start.md
docs/testing_and_debugging.md
docs/ultra_rapid_start.md
docs/archive/README.md
docs/archive/2026-04-pre-rewrite/README.md
docs/archive/2026-04-pre-rewrite/README.md.bland
docs/archive/2026-04-pre-rewrite/docs/DAY_EC_ENVIRONMENT.md
docs/archive/2026-04-pre-rewrite/docs/legacy_code_to_remove.md
docs/archive/2026-04-pre-rewrite/docs/operations.md
docs/archive/2026-04-pre-rewrite/docs/overview.md
docs/archive/2026-04-pre-rewrite/docs/pip_install.md
docs/archive/2026-04-pre-rewrite/docs/quickest_start.md
docs/archive/2026-04-pre-rewrite/docs/ultra_rapid_start.md
docs/archive/legacy/README.md
docs/archive/legacy-dayoa-env/conda_base.yaml
docs/archive/legacy-dayoa-env/day.yaml
docs/archive/legacy-dayoa-env/day_env_installer.sh
etc/.DS_Store
etc/analysis_samples_template.tsv
etc/fsx_export.yaml
logs/.hold
tests/__init__.py
tests/test_activate.py
tests/test_aws_context.py
tests/test_budgets.py
tests/test_cli_registry_v2.py
tests/test_cloudformation.py
tests/test_cluster_info.py
tests/test_config_sources.py
tests/test_delete.py
tests/test_drift.py
tests/test_ec2.py
tests/test_environment_contract.py
tests/test_export.py
tests/test_headnode_init.py
tests/test_heartbeat.py
tests/test_iam.py
tests/test_install_miniconda.py
tests/test_monitor.py
tests/test_packaged_defaults.py
tests/test_preflight_report.py
tests/test_pricing_snapshots.py
tests/test_quotas.py
tests/test_renderer.py
tests/test_resources_extraction.py
tests/test_runner.py
tests/test_s3.py
tests/test_script_entrypoints.py
tests/test_spot_pricing.py
tests/test_ssm.py
tests/test_ssm_e2e_runner.py
tests/test_stage_samples_from_local_to_headnode.py
tests/test_state_store.py
tests/test_supported_no_pem_refs.py
tests/test_triplets.py
tests/test_versioning.py
tests/test_workflow.py