AGENTS.md
LICENSE
activate
environment.yaml
pyproject.toml
setup.py
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-cfg-headnode
bin/daylily-create-ephemeral-cluster
bin/daylily-ensure-sns-permissions
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-omics-analysis-headnode
bin/daylily-ssh-into-headnode
bin/daylily-ssh-to-ssm-e2e
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/headnode_utils/daylily-github-credential
bin/headnode_utils/sq
bin/headnode_utils/sqq
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/upload_s3_rclone_w_tags.sh
bin/helpers/watch_slurm.sh
bin/other/print_spot_interruptions.sh
bin/other/regsub_yaml.sh
bin/util/bash_sleep.sh
bin/util/benchmark_filesystem.sh
bin/util/capture_baseline.py
bin/util/col_error.bash
bin/util/grep_tab.sh
bin/util/profile_freshness_warn.bash
bin/util/shfmt
bin/util/user_pays.json
bin/utils/ilmn/extract_undetermined_indexes
config/baseline-cluster-request.yaml
config/command_catalog_performance_history.json
config/daylily_available_repositories.yaml
config/daylily_cli_global.yaml
config/daylily_ephemeral_cluster_cmdcat_10_0_103_all_20260707.yaml
config/daylily_ephemeral_cluster_dragain10_20260710.yaml
config/daylily_ephemeral_cluster_dragain11_20260710.yaml
config/daylily_ephemeral_cluster_dragain12_20260710.yaml
config/daylily_ephemeral_cluster_dragen_103_pg_20260707.yaml
config/daylily_ephemeral_cluster_dragen_fix2_20260708.yaml
config/daylily_ephemeral_cluster_dragen_fix3_20260708.yaml
config/daylily_ephemeral_cluster_dragen_fix4_20260708.yaml
config/daylily_ephemeral_cluster_dragen_fix5_20260708.yaml
config/daylily_ephemeral_cluster_dragen_fix_20260708.yaml
config/daylily_ephemeral_cluster_dragen_na19235_20260707.yaml
config/daylily_ephemeral_cluster_dragen_native_ami_rhel8_2c.yaml
config/daylily_ephemeral_cluster_dragen_native_ami_rhel8_2c_nofsx.yaml
config/daylily_ephemeral_cluster_dragen_native_ami_rhel8_2c_public.yaml
config/daylily_ephemeral_cluster_dragen_pcluster_image_rhel8_2c.yaml
config/daylily_ephemeral_cluster_dragen_pcluster_image_rhel8_2c_fsx.yaml
config/daylily_ephemeral_cluster_dragen_pcluster_image_rhel8_2c_nofsx.yaml
config/daylily_ephemeral_cluster_ifx_p2_1000_120_20260715.yaml
config/daylily_ephemeral_cluster_ifx_p2_250_20260714.yaml
config/daylily_ephemeral_cluster_sentieon_single_hg003_5x_20260712.yaml
config/daylily_ephemeral_cluster_template.yaml
config/daylily_ephemeral_cost_config.yaml
config/daylily_pipeline_command_catalog.yaml
config/dragen_fix5_repo_overrides.txt
config/example-cluster-request.yaml
config/github_known_hosts
config/pclu-2100_create_20261014T200659Z.yaml
config/product_matrix_command_catalog.json
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/daylily_reference_version_0.7.131c.info
config/day_cluster/fsx_node_health.py
config/day_cluster/fsx_node_health_policy.json
config/day_cluster/install_apptainer_rhel8.sh
config/day_cluster/install_fsx_node_health.sh
config/day_cluster/install_slurm_ipc_policy.sh
config/day_cluster/install_slurm_job_submit_policy.sh
config/day_cluster/job_submit.lua
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_almalinux8_dragen.sh
config/day_cluster/post_install_rhel8_dragen.sh
config/day_cluster/post_install_tags.sh
config/day_cluster/post_install_ubuntu_combined.sh
config/day_cluster/prepare_rhel8_cpu_nvme.sh
config/day_cluster/prod_cluster_dragen_native_ami_rhel8.yaml
config/day_cluster/prod_cluster_dragen_native_ami_rhel8_nofsx.yaml
config/day_cluster/prod_cluster_dragen_pcluster_image_rhel8.yaml
config/day_cluster/prod_cluster_dragen_pcluster_image_rhel8_nofsx.yaml
config/day_cluster/s3_ref_data.versions
config/day_cluster/sbatch
config/day_cluster/sequencing_inputs.py
config/day_cluster/shutdown_script_ubuntu_head.sh
config/day_cluster/shutdown_ubuntu.sh
config/day_cluster/sleep_test.sh
config/day_cluster/slurm_accounting_mysql_ec2.yml
config/day_cluster/slurm_accounting_privatelink.yml
config/day_cluster/archive_do_not_use/cromwell_test.yaml
config/day_cluster/archive_do_not_use/prod_cluster.yaml
config/day_cluster/archive_do_not_use/prod_cluster_dragen.yaml
config/day_cluster/archive_do_not_use/prod_cluster_nested_spot_mem_scratch.yaml
config/day_cluster/archive_do_not_use/prod_cluster_v8.yaml
config/day_cluster/archive_do_not_use/prod_cluster_variant.yaml
config/day_cluster/archive_do_not_use/regions/all_clusters.yaml
config/day_cluster/dragen/us-west-2/us-west-2b/prod_cluster_dragen_us-west-2b.yaml
config/day_cluster/intel/ap-south-1/ap-south-1a/prod_cluster_intel_ondemand_ap-south-1a.yaml
config/day_cluster/intel/ap-south-1/ap-south-1a/prod_cluster_intel_spot_ap-south-1a.yaml
config/day_cluster/intel/ap-south-1/ap-south-1b/prod_cluster_intel_ondemand_ap-south-1b.yaml
config/day_cluster/intel/ap-south-1/ap-south-1b/prod_cluster_intel_spot_ap-south-1b.yaml
config/day_cluster/intel/ap-south-1/ap-south-1c/prod_cluster_intel_ondemand_ap-south-1c.yaml
config/day_cluster/intel/ap-south-1/ap-south-1c/prod_cluster_intel_spot_ap-south-1c.yaml
config/day_cluster/intel/eu-central-1/eu-central-1a/prod_cluster_intel_ondemand_eu-central-1a.yaml
config/day_cluster/intel/eu-central-1/eu-central-1a/prod_cluster_intel_spot_eu-central-1a.yaml
config/day_cluster/intel/eu-central-1/eu-central-1b/prod_cluster_intel_ondemand_eu-central-1b.yaml
config/day_cluster/intel/eu-central-1/eu-central-1b/prod_cluster_intel_spot_eu-central-1b.yaml
config/day_cluster/intel/eu-central-1/eu-central-1c/prod_cluster_intel_ondemand_eu-central-1c.yaml
config/day_cluster/intel/eu-central-1/eu-central-1c/prod_cluster_intel_spot_eu-central-1c.yaml
config/day_cluster/intel/us-east-2/us-east-2a/prod_cluster_intel_ondemand_us-east-2a.yaml
config/day_cluster/intel/us-east-2/us-east-2a/prod_cluster_intel_spot_us-east-2a.yaml
config/day_cluster/intel/us-east-2/us-east-2b/prod_cluster_intel_ondemand_us-east-2b.yaml
config/day_cluster/intel/us-east-2/us-east-2b/prod_cluster_intel_spot_us-east-2b.yaml
config/day_cluster/intel/us-east-2/us-east-2c/prod_cluster_intel_ondemand_us-east-2c.yaml
config/day_cluster/intel/us-east-2/us-east-2c/prod_cluster_intel_spot_us-east-2c.yaml
config/day_cluster/intel/us-west-1/us-west-1a/prod_cluster_intel_ondemand_us-west-1a.yaml
config/day_cluster/intel/us-west-1/us-west-1a/prod_cluster_intel_spot_us-west-1a.yaml
config/day_cluster/intel/us-west-1/us-west-1b/prod_cluster_intel_ondemand_us-west-1b.yaml
config/day_cluster/intel/us-west-1/us-west-1b/prod_cluster_intel_spot_us-west-1b.yaml
config/day_cluster/intel/us-west-2/us-west-2a/prod_cluster_intel_ondemand_us-west-2a.yaml
config/day_cluster/intel/us-west-2/us-west-2a/prod_cluster_intel_spot_us-west-2a.yaml
config/day_cluster/intel/us-west-2/us-west-2b/prod_cluster_intel_ondemand_us-west-2b.yaml
config/day_cluster/intel/us-west-2/us-west-2b/prod_cluster_intel_spot_us-west-2b.yaml
config/day_cluster/intel/us-west-2/us-west-2c/prod_cluster_intel_ondemand_us-west-2c.yaml
config/day_cluster/intel/us-west-2/us-west-2c/prod_cluster_intel_spot_us-west-2c.yaml
config/day_cluster/intel/us-west-2/us-west-2d/prod_cluster_intel_ondemand_us-west-2d.yaml
config/day_cluster/intel/us-west-2/us-west-2d/prod_cluster_intel_spot_us-west-2d.yaml
config/day_cluster/rhel/eu-central-1/eu-central-1b/prod_cluster_rhel_eu-central-1b.yaml
config/day_cluster/rhel/eu-central-1/eu-central-1c/prod_cluster_rhel_eu-central-1c.yaml
config/day_cluster/rhel/us-west-2/us-west-2b/prod_cluster_rhel_us-west-2b.yaml
config/day_cluster/rhel/us-west-2/us-west-2c/prod_cluster_rhel_us-west-2c.yaml
config/day_cluster/sentieon-single/us-west-2/us-west-2c/prod_cluster_sentieon-single_us-west-2c.yaml
config/iam/pcluster_node_artifacts_read.json
config/imagebuilder/almalinux8_public_pcluster316_develop.yaml
config/imagebuilder/dragen_el8_4_5_4_pcluster315.yaml
config/monitoring/hg002a-series23-20260914t002003z/README.md
config/monitoring/hg002a-series23-20260914t002003z/availability-20260914T045107Z.json
config/monitoring/hg002a-series23-20260914t002003z/availability-20260914T045107Z.md
config/monitoring/hg002a-series23-20260914t002003z/controller-target.json
config/monitoring/hg002a-series23-20260914t002003z/dry-terminal.json
config/monitoring/hg002a-series23-20260914t002003z/identity.json
config/monitoring/hg002a-series23-20260914t002003z/progress-20260914T0522-interactive.json
config/monitoring/hg002a-series23-20260914t002003z/progress-20260914T0522-interactive.md
config/monitoring/hg002a-series23-20260914t002003z/progress-baseline.json
config/monitoring/hg002a-series23-20260914t002003z/sampling_matrix.json
config/monitoring/hg002a-series23-20260914t002003z/progress-20260914T012244Z/fsx.stderr
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config/monitoring/hg002a-series23-20260914t002003z/progress-20260914T012244Z/report.md
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config/monitoring/hg002a-series23-20260914t002003z/progress-20260914T055743Z/report.md
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config/monitoring/hg002a-series23-20260914t002003z/progress-20260914T055743Z/workflow-status.stderr
config/operational/dragen_pcluster315_almalinux8_20260710.yaml
config/operational/lsmc_dragen_us_west_2b_max12/README.md
config/operational/lsmc_dragen_us_west_2b_max12/dyec-create.template.yaml
config/operational/lsmc_dragen_us_west_2b_max12/pcluster.max12.reference.yaml
config/operational/lsmc_dragen_us_west_2b_nvme_max8/README.md
config/operational/lsmc_dragen_us_west_2b_nvme_max8/dyec-create.template.yaml
config/operational/lsmc_dragen_us_west_2b_nvme_max8/pcluster.nvme-max8.reference.yaml
config/templates/sentieon_license_server_usw2d_cloudformation.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/analysis_identity.py
daylily_ec/analysis_lock.py
daylily_ec/analysis_recovery.py
daylily_ec/analysis_status.py
daylily_ec/bjuice_crosswalk_run_config.py
daylily_ec/bjuice_preval_config.py
daylily_ec/bjuice_v2_hg002_multi_au_config.py
daylily_ec/bjuice_validation_config.py
daylily_ec/campaign_target.py
daylily_ec/catalog_validation.py
daylily_ec/cli.py
daylily_ec/cli_context.py
daylily_ec/cluster_inspection.py
daylily_ec/cluster_monitor.py
daylily_ec/cockpit.py
daylily_ec/command_catalog_performance.py
daylily_ec/command_sample_stats.py
daylily_ec/complete_genomics_manifest.py
daylily_ec/concordance_config.py
daylily_ec/cost_allocation.py
daylily_ec/cost_center_refresh.py
daylily_ec/cost_context.py
daylily_ec/cost_controls.py
daylily_ec/create.py
daylily_ec/execution_status.py
daylily_ec/export_attempts.py
daylily_ec/export_changes.py
daylily_ec/export_directory_metadata.py
daylily_ec/export_inventory.py
daylily_ec/fsx_cli.py
daylily_ec/fsx_node_health_cli.py
daylily_ec/fsx_node_probe.py
daylily_ec/fsx_telemetry.py
daylily_ec/headnode.py
daylily_ec/headnode_config_inputs.py
daylily_ec/headnode_control.py
daylily_ec/headnode_observability.py
daylily_ec/headnode_readiness.py
daylily_ec/headnode_receipts.py
daylily_ec/identity_receipts.py
daylily_ec/manifest_set.py
daylily_ec/matrix_cli.py
daylily_ec/matrix_ingestion.py
daylily_ec/operations_management.py
daylily_ec/overview.py
daylily_ec/overview_cli.py
daylily_ec/presentation.py
daylily_ec/product_matrix_catalog.py
daylily_ec/product_matrix_runtime.py
daylily_ec/prompt_status.py
daylily_ec/repositories.py
daylily_ec/run_mount_cache.py
daylily_ec/run_mounts.py
daylily_ec/runtime_cache_export.py
daylily_ec/sequencing_data.py
daylily_ec/spot_price_logs.py
daylily_ec/ssh_to_ssm_e2e_runner.py
daylily_ec/stage_samples.py
daylily_ec/tests_runner.py
daylily_ec/themes.py
daylily_ec/ui.py
daylily_ec/version_policy.py
daylily_ec/versioning.py
daylily_ec/workflow_continuation.py
daylily_ec/workflow_observability.py
daylily_ec/workflow_postrun.py
daylily_ec/workflow_reconciliation.py
daylily_ec/artifacts/__init__.py
daylily_ec/aws/__init__.py
daylily_ec/aws/api_call_audit.py
daylily_ec/aws/billing_read_guard.py
daylily_ec/aws/budgets.py
daylily_ec/aws/capacity_snapshot.py
daylily_ec/aws/cloudformation.py
daylily_ec/aws/cluster_tags.py
daylily_ec/aws/context.py
daylily_ec/aws/cost_centers.py
daylily_ec/aws/cur.py
daylily_ec/aws/cur_export.py
daylily_ec/aws/dragen_license.py
daylily_ec/aws/ec2.py
daylily_ec/aws/fsx_network.py
daylily_ec/aws/fsx_persistent2.py
daylily_ec/aws/github_deploy_key.py
daylily_ec/aws/github_deploy_key_secret.py
daylily_ec/aws/heartbeat.py
daylily_ec/aws/iam.py
daylily_ec/aws/idle_cost.py
daylily_ec/aws/on_demand_cost_report.py
daylily_ec/aws/pricing_snapshots.py
daylily_ec/aws/quotas.py
daylily_ec/aws/resize_slurm_accounting.py
daylily_ec/aws/s3.py
daylily_ec/aws/s3_presign.py
daylily_ec/aws/sentieon_license.py
daylily_ec/aws/sentieon_license_network.py
daylily_ec/aws/sentieon_license_server.py
daylily_ec/aws/slurm_accounting.py
daylily_ec/aws/slurm_accounting_privatelink.py
daylily_ec/aws/spot_pricing.py
daylily_ec/aws/ssm.py
daylily_ec/aws/validation.py
daylily_ec/config/__init__.py
daylily_ec/config/cluster_requests.py
daylily_ec/config/models.py
daylily_ec/config/triplets.py
daylily_ec/matrix_renderer/UPSTREAM.json
daylily_ec/matrix_renderer/__init__.py
daylily_ec/matrix_renderer/generator_core.py
daylily_ec/matrix_renderer/spec_summary.py
daylily_ec/matrix_renderer/assets/viridis.json
daylily_ec/matrix_renderer/assets/fonts/advance_widths.json
daylily_ec/pcluster/__init__.py
daylily_ec/pcluster/backport.py
daylily_ec/pcluster/monitor.py
daylily_ec/pcluster/runner.py
daylily_ec/render/__init__.py
daylily_ec/render/renderer.py
daylily_ec/render/storage.py
daylily_ec/resources/__init__.py
daylily_ec/resources/contracts.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-cfg-headnode
daylily_ec/resources/payload/bin/daylily-create-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-omics-analysis-headnode
daylily_ec/resources/payload/bin/daylily-ssh-into-headnode
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/headnode_utils/daylily-github-credential
daylily_ec/resources/payload/bin/headnode_utils/sq
daylily_ec/resources/payload/bin/headnode_utils/sqq
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/upload_s3_rclone_w_tags.sh
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/daylily_pipeline_command_catalog.yaml
daylily_ec/resources/payload/config/github_known_hosts
daylily_ec/resources/payload/config/product_matrix_command_catalog.json
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/daylily_reference_version_0.7.131c.info
daylily_ec/resources/payload/config/day_cluster/fsx_node_health.py
daylily_ec/resources/payload/config/day_cluster/fsx_node_health_policy.json
daylily_ec/resources/payload/config/day_cluster/install_apptainer_rhel8.sh
daylily_ec/resources/payload/config/day_cluster/install_fsx_node_health.sh
daylily_ec/resources/payload/config/day_cluster/install_slurm_ipc_policy.sh
daylily_ec/resources/payload/config/day_cluster/install_slurm_job_submit_policy.sh
daylily_ec/resources/payload/config/day_cluster/job_submit.lua
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_almalinux8_dragen.sh
daylily_ec/resources/payload/config/day_cluster/post_install_rhel8_dragen.sh
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/prepare_rhel8_cpu_nvme.sh
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/sequencing_inputs.py
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/slurm_accounting_mysql_ec2.yml
daylily_ec/resources/payload/config/day_cluster/slurm_accounting_privatelink.yml
daylily_ec/resources/payload/config/day_cluster/archive_do_not_use/cromwell_test.yaml
daylily_ec/resources/payload/config/day_cluster/archive_do_not_use/prod_cluster.yaml
daylily_ec/resources/payload/config/day_cluster/archive_do_not_use/prod_cluster_dragen.yaml
daylily_ec/resources/payload/config/day_cluster/archive_do_not_use/prod_cluster_v8.yaml
daylily_ec/resources/payload/config/day_cluster/archive_do_not_use/prod_cluster_variant.yaml
daylily_ec/resources/payload/config/day_cluster/archive_do_not_use/regions/all_clusters.yaml
daylily_ec/resources/payload/config/day_cluster/dragen/us-west-2/us-west-2b/prod_cluster_dragen_us-west-2b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/ap-south-1/ap-south-1a/prod_cluster_intel_ondemand_ap-south-1a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/ap-south-1/ap-south-1a/prod_cluster_intel_spot_ap-south-1a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/ap-south-1/ap-south-1b/prod_cluster_intel_ondemand_ap-south-1b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/ap-south-1/ap-south-1b/prod_cluster_intel_spot_ap-south-1b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/ap-south-1/ap-south-1c/prod_cluster_intel_ondemand_ap-south-1c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/ap-south-1/ap-south-1c/prod_cluster_intel_spot_ap-south-1c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/eu-central-1/eu-central-1a/prod_cluster_intel_ondemand_eu-central-1a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/eu-central-1/eu-central-1a/prod_cluster_intel_spot_eu-central-1a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/eu-central-1/eu-central-1b/prod_cluster_intel_ondemand_eu-central-1b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/eu-central-1/eu-central-1b/prod_cluster_intel_spot_eu-central-1b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/eu-central-1/eu-central-1c/prod_cluster_intel_ondemand_eu-central-1c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/eu-central-1/eu-central-1c/prod_cluster_intel_spot_eu-central-1c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-east-2/us-east-2a/prod_cluster_intel_ondemand_us-east-2a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-east-2/us-east-2a/prod_cluster_intel_spot_us-east-2a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-east-2/us-east-2b/prod_cluster_intel_ondemand_us-east-2b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-east-2/us-east-2b/prod_cluster_intel_spot_us-east-2b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-east-2/us-east-2c/prod_cluster_intel_ondemand_us-east-2c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-east-2/us-east-2c/prod_cluster_intel_spot_us-east-2c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-1/us-west-1a/prod_cluster_intel_ondemand_us-west-1a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-1/us-west-1a/prod_cluster_intel_spot_us-west-1a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-1/us-west-1b/prod_cluster_intel_ondemand_us-west-1b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-1/us-west-1b/prod_cluster_intel_spot_us-west-1b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2a/prod_cluster_intel_ondemand_us-west-2a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2a/prod_cluster_intel_spot_us-west-2a.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2b/prod_cluster_intel_ondemand_us-west-2b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2b/prod_cluster_intel_spot_us-west-2b.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2c/prod_cluster_intel_ondemand_us-west-2c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2c/prod_cluster_intel_spot_us-west-2c.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2d/prod_cluster_intel_ondemand_us-west-2d.yaml
daylily_ec/resources/payload/config/day_cluster/intel/us-west-2/us-west-2d/prod_cluster_intel_spot_us-west-2d.yaml
daylily_ec/resources/payload/config/day_cluster/rhel/eu-central-1/eu-central-1b/prod_cluster_rhel_eu-central-1b.yaml
daylily_ec/resources/payload/config/day_cluster/rhel/eu-central-1/eu-central-1c/prod_cluster_rhel_eu-central-1c.yaml
daylily_ec/resources/payload/config/day_cluster/rhel/us-west-2/us-west-2b/prod_cluster_rhel_us-west-2b.yaml
daylily_ec/resources/payload/config/day_cluster/rhel/us-west-2/us-west-2c/prod_cluster_rhel_us-west-2c.yaml
daylily_ec/resources/payload/config/day_cluster/sentieon-single/us-west-2/us-west-2c/prod_cluster_sentieon-single_us-west-2c.yaml
daylily_ec/resources/payload/etc/analysis_samples_template.tsv
daylily_ec/resources/payload/etc/fsx_export.yaml
daylily_ec/resources/payload/examples/catalog/apply_product_matrix_runtime_policy.py
daylily_ec/resources/payload/examples/catalog/build_product_matrix_runtime.py
daylily_ec/resources/payload/examples/catalog/illumina_kitchensink_runtime.yaml
daylily_ec/resources/payload/examples/catalog/product_matrix_hg002_runtime.yaml
daylily_ec/resources/payload/examples/catalog/hg002_solo36/README.md
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/README.md
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/ashg-etc-campaign-context.json
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/asset_distribution.json
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/hg002_ilmn60x_ont10x_hybrid_pangenome.yaml
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/hg002_ont10x_pangenome_preparation.yaml
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/hg002_ultima30x_ont10x_pangenome_preparation.yaml
daylily_ec/resources/payload/examples/catalog/hybrid_pangenome/hg002_ultima_ont_hybrid_pangenome.yaml
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/libraries.tsv
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/samples.tsv
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/specimens.tsv
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_six_manifest_v1/staging_receipt.json
daylily_ec/resources/payload/examples/staging/complete_genomics_solo_slim_mounted_reference_v1/analysis_samples_manifest.tsv
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/input_identity.json
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/samples.tsv
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_bjuice_verified_5x5x_fastq/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/README.md
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/analysis_samples_manifest.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/analysis_units.tsv
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daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/samples.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_complete_genomics/staging_receipt.json
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/samples.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/source_binding.json
daylily_ec/resources/payload/examples/staging/hg002_slim_illumina/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/samples.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/source_binding.json
daylily_ec/resources/payload/examples/staging/hg002_slim_ont/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/samples.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/source_binding.json
daylily_ec/resources/payload/examples/staging/hg002_slim_ultima/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg003_hiomrs_1x_raw_fastq/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg003_hiomrs_1x_raw_fastq/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg003_hiomrs_1x_raw_fastq/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg003_hiomrs_1x_raw_fastq/samples.tsv
daylily_ec/resources/payload/examples/staging/hg003_hiomrs_1x_raw_fastq/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg003_hiomrs_1x_raw_fastq/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/analysis_samples_manifest.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/samples.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/source_binding.json
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/specimens.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_complete_genomics/staging_receipt.json
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/analysis_unit_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/analysis_units.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/libraries.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/samples.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/sequencing_inputs.tsv
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/source_binding.json
daylily_ec/resources/payload/examples/staging/hg003_slim_ultima/specimens.tsv
daylily_ec/scripts/__init__.py
daylily_ec/scripts/common.py
daylily_ec/scripts/daylily_cfg_headnode.py
daylily_ec/scripts/daylily_run_omics_analysis_headnode.py
daylily_ec/scripts/daylily_ssh_into_headnode.py
daylily_ec/slurm/__init__.py
daylily_ec/slurm/sacct.py
daylily_ec/state/__init__.py
daylily_ec/state/drift.py
daylily_ec/state/finalize_accounting.py
daylily_ec/state/models.py
daylily_ec/state/recover_create.py
daylily_ec/state/slurm_accounting.py
daylily_ec/state/store.py
daylily_ec/util/__init__.py
daylily_ec/workflow/__init__.py
daylily_ec/workflow/accounting_secret_access.py
daylily_ec/workflow/attach_slurm_accounting.py
daylily_ec/workflow/cluster_instance_exclusions.py
daylily_ec/workflow/cluster_max_count.py
daylily_ec/workflow/cluster_queue_update.py
daylily_ec/workflow/compute_fleet.py
daylily_ec/workflow/cpu_queue_handoff.py
daylily_ec/workflow/create_cluster.py
daylily_ec/workflow/create_request.py
daylily_ec/workflow/delete_cluster.py
daylily_ec/workflow/dyr_preflight.py
daylily_ec/workflow/export_data.py
daylily_ec/workflow/inspect_slurm_accounting.py
daylily_ec/workflow/linked_fsx_tags.py
daylily_ec/workflow/postcreate_slurm_accounting.py
daylily_ec/workflow/recover_slurm_accounting.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/scm_file_list.json
daylily_ephemeral_cluster.egg-info/scm_version.json
daylily_ephemeral_cluster.egg-info/top_level.txt
docs/release_22.0.3.md
docs/release_22.0.6.md
docs/workflow_failed_attempt_reconciliation.md
docs/plans/20261031T234800Z_bootstrap_apt_reliability_ledger.md
etc/.DS_Store
etc/analysis_samples_template.tsv
etc/fsx_export.yaml