Path	Lines of Code
api/build.gradle	175
api/pipeline.sh	1
api/profiles.gradle	22
billing-report-agent/build.gradle	65
build.gradle	186
client/build.gradle	33
client/config/webpack.config.js	379
cloud-pipeline-common/build.gradle	1
cloud-pipeline-common/event-sourcing-java-client/build.gradle	28
cloud-pipeline-common/model/build.gradle	60
cloud-pipeline-webdav-client/build.gradle	53
cloud-pipeline-webdav-client/build_cli.sh	38
cloud-pipeline-webdav-client/build_linux.sh	41
cloud-pipeline-webdav-client/build_win.sh	39
cloud-pipeline-webdav-client/scripts/update-darwin.sh	1
cloud-pipeline-webdav-client/scripts/update-linux.sh	1
cloud-pipeline-webdav-client/src/main/webpack.config.js	30
cloud-pipeline-webdav-client/src/renderer/webpack.config.js	20
core/build.gradle	34
data-sharing-service/api/build.gradle	53
data-sharing-service/build.gradle	10
data-sharing-service/client/build.gradle	29
data-sharing-service/client/config/webpack.common.js	83
data-sharing-service/client/config/webpack.dev.js	98
data-sharing-service/client/config/webpack.prod.js	116
data-transfer-service/build.gradle	163
data-transfer-service/src/main/resources/qsub.sh	12
deploy/appveyor/appveyor_build_macos.sh	19
deploy/appveyor/appveyor_build_macos_arm.sh	21
deploy/appveyor/appveyor_pack_dist.sh	58
deploy/appveyor/appveyor_publish_docs.sh	28
deploy/build.sh	166
deploy/contents/install/app/configure-utils.sh	1379
deploy/contents/install/app/docker-utils.sh	113
deploy/contents/install/app/format-utils.sh	16
deploy/contents/install/app/install-common.sh	23
deploy/contents/install/app/install-master.sh	140
deploy/contents/install/app/install-utils.sh	1520
deploy/contents/install/app/install.sh	1183
deploy/contents/scrap/app/get_configmap.sh	17
deploy/contents/scrap/app/get_pref.sh	7
deploy/contents/scrap/app/get_services.sh	26
deploy/contents/scrap/app/get_tools.sh	105
deploy/contents/scrap/app/get_users.sh	27
deploy/contents/scrap/app/get_version.sh	7
deploy/contents/scrap/app/scrap.sh	199
deploy/contents/scrap/app/utils.sh	30
deploy/contents/sync/app/sync.sh	159
deploy/docker/build-dockers.sh	280
deploy/docker/cp-api-srv/liveness-api-srv-template.sh	11
deploy/docker/cp-api-srv/liveness-git-sync.sh	13
deploy/docker/cp-bkp-worker/backup.sh	133
deploy/docker/cp-bkp-worker/backupers/cp-api-db-bkp.sh	4
deploy/docker/cp-bkp-worker/backupers/cp-api-srv-bkp.sh	11
deploy/docker/cp-bkp-worker/backupers/cp-git-bkp.sh	27
deploy/docker/cp-clair-v4/update_config.sh	42
deploy/docker/cp-clair/update_config.sh	66
deploy/docker/cp-dav/liveness.sh	14
deploy/docker/cp-dav/sync/nfs-watcher.sh	7
deploy/docker/cp-dav/sync/sync-nfs.sh	34
deploy/docker/cp-deployment-autoscaler/init_multicloud.sh	83
deploy/docker/cp-docker-registry/docker-entrypoint.sh	6
deploy/docker/cp-docker-registry/update_config.sh	105
deploy/docker/cp-docker-registry/update_nginx_config.sh	61
deploy/docker/cp-dts/dts.sh	4
deploy/docker/cp-dts/qsub.sh	12
deploy/docker/cp-edge/crontab.sh	5
deploy/docker/cp-edge/liveness.sh	8
deploy/docker/cp-edge/maintenance/scripts/crontab.sh	5
deploy/docker/cp-edge/maintenance/scripts/maintenance.sh	1
deploy/docker/cp-edge/maintenance/ui/webpack.config.js	173
deploy/docker/cp-edge/sync-routes.sh	1
deploy/docker/cp-git/gitlab-runner-scripts/cleanup.sh	63
deploy/docker/cp-git/gitlab-runner-scripts/init-gitlab-runner.sh	125
deploy/docker/cp-git/gitlab-runner-scripts/prepare.sh	52
deploy/docker/cp-git/gitlab-runner-scripts/run.sh	75
deploy/docker/cp-git/update_config.sh	184
deploy/docker/cp-git/update_config_v17.sh	183
deploy/docker/cp-gitlab-reader/init.sh	5
deploy/docker/cp-node-reporter/oom/reporter.sh	165
deploy/docker/cp-notifier/liveness.sh	5
deploy/docker/cp-search-elk/get-aws-profile.sh	108
deploy/docker/cp-search-elk/init.sh	182
deploy/docker/cp-search/liveness.sh	5
deploy/docker/cp-storage-lifecycle-service/liveness.sh	5
deploy/docker/cp-storage-lifecycle-service/start.sh	27
deploy/docker/cp-tools/base/aws-healthomics-workflow/omics-utils/omics_container_syncronizer.sh	183
deploy/docker/cp-tools/base/aws-healthomics-workflow/omics-utils/omics_workflow_builder.sh	311
deploy/docker/cp-tools/base/cromwell/cromwell_submit_task.sh	98
deploy/docker/cp-tools/base/desktop/noVNC/launchers/create_chrome_launcher.sh	17
deploy/docker/cp-tools/base/desktop/noVNC/scripts/install/no_vnc.sh	11
deploy/docker/cp-tools/base/desktop/noVNC/scripts/install/set_user_permission.sh	8
deploy/docker/cp-tools/base/desktop/noVNC/scripts/startup/start.sh	34
deploy/docker/cp-tools/base/desktop/noVNC/scripts/startup/vnc_startup.sh	38
deploy/docker/cp-tools/base/desktop/noVNC/scripts/startup/wm_startup.sh	8
deploy/docker/cp-tools/base/desktop/nomachine/centos/scripts/install_git.sh	20
deploy/docker/cp-tools/base/desktop/nomachine/centos/scripts/libreoffice.sh	8
deploy/docker/cp-tools/base/desktop/nomachine/create_chrome_launcher.sh	15
deploy/docker/cp-tools/base/desktop/nomachine/nomachine_launcher.sh	39
deploy/docker/cp-tools/base/desktop/nomachine/ubuntu/scripts/libreoffice.sh	3
deploy/docker/cp-tools/base/jupyter-lab/start.sh	55
deploy/docker/cp-tools/base/jupyter/anaconda_install.sh	6
deploy/docker/cp-tools/base/jupyter/anaconda_install_python.sh	11
deploy/docker/cp-tools/base/jupyter/anaconda_install_r.sh	9
deploy/docker/cp-tools/base/jupyter/start.sh	13
deploy/docker/cp-tools/base/rstudio/post_commit.sh	8
deploy/docker/cp-tools/base/rstudio/start.sh	39
deploy/docker/cp-tools/base/ubi/dcv/start.sh	77
deploy/docker/cp-tools/base/ubi/nomachine/create_chrome_launcher.sh	15
deploy/docker/cp-tools/base/ubi/nomachine/nomachine_launcher.sh	39
deploy/docker/cp-tools/md/namd/install/install_common_packages.sh	19
deploy/docker/cp-tools/md/namd/install/install_namd_binaries.sh	11
deploy/docker/cp-tools/md/namd/install/install_namd_sources.sh	30
deploy/docker/cp-tools/md/namd/install/install_vmd_binaries.sh	11
deploy/docker/cp-tools/md/namd/launchers/create_nedit_launcher.sh	11
deploy/docker/cp-tools/md/namd/launchers/create_vmd_launcher.sh	11
deploy/docker/cp-tools/ngs/cellranger/install_bcl2fastq18.sh	44
deploy/docker/cp-tools/ngs/cellranger/install_bcl2fastq2.sh	34
deploy/docker/cp-tools/ngs/cellranger/install_cr_versions.sh	39
deploy/docker/cp-tools/research/cellprofiler-web-api/start.sh	136
deploy/docker/cp-tools/research/hcs-parser/convert_to_ome_tiff.sh	49
deploy/docker/cp-tools/research/hcs-parser/start.sh	3
deploy/docker/cp-tools/research/hcs-parser/start_cluster.sh	5
deploy/docker/cp-tools/research/phaedra/configure_phaedra.sh	14
deploy/docker/cp-tools/research/phaedra/create_phaedra_launcher.sh	13
deploy/docker/cp-tools/research/qupath/create_qupath_launcher.sh	11
deploy/docker/cp-tools/research/qupath/qupath.sh	27
deploy/docker/cp-tools/research/qupath/qupath_install.sh	4
deploy/docker/cp-tools/research/spyder/anaconda_install.sh	10
deploy/docker/cp-tools/research/spyder/create_spyder_launcher.sh	11
deploy/docker/cp-tools/research/spyder/spyder.sh	5
deploy/docker/cp-tools/research/wsi-parser/create_deepzoom.sh	91
deploy/docker/cp-tools/research/wsi-parser/create_pyramid_ome_tiff.sh	104
deploy/docker/cp-tools/research/wsi-parser/start.sh	3
deploy/docker/cp-volume-monitor/check.sh	105
deploy/github_actions/gha_build_client.sh	11
deploy/github_actions/gha_build_cloud_data_linux.sh	10
deploy/github_actions/gha_build_cloud_data_windows.sh	10
deploy/github_actions/gha_build_data_sharing_service.sh	10
deploy/github_actions/gha_build_data_transfer_service.sh	16
deploy/github_actions/gha_build_fs_browser.sh	10
deploy/github_actions/gha_build_gpu_stat.sh	10
deploy/github_actions/gha_build_pipe_linux.sh	13
deploy/github_actions/gha_build_pipe_linux_el6.sh	14
deploy/github_actions/gha_build_pipe_macos.sh	13
deploy/github_actions/gha_build_pipe_windows.sh	11
deploy/github_actions/gha_pack_dist.sh	104
deploy/infra/aws/cloudformation/create_assets_zip.sh	22
deploy/infra/aws/install-common-node.sh	58
deploy/infra/aws/install-gpu-node.sh	67
deploy/infra/az/install-common-node.sh	66
deploy/infra/az/install-gpu-node-a100.sh	94
deploy/infra/az/install-gpu-node.sh	82
deploy/infra/build-infra.sh	620
deploy/infra/gcp/install-common-node.sh	65
deploy/infra/gcp/install-gpu-node.sh	90
deploy/jenkins/jenkins-docker/checkout_url.sh	41
deploy/jenkins/jenkins-docker/init.groovy	15
deploy/jenkins/jenkins-jobs/build-pipectl/build-pipectl.sh	23
deploy/jenkins/jenkins-jobs/build-pipectl/script.sh	26
deploy/jenkins/jenkins-jobs/deploy-dev-aws/prepare-assets.sh	45
deploy/jenkins/jenkins-jobs/deploy-dev-aws/run-pipectl.sh	85
deploy/jenkins/jenkins-jobs/deploy-dev-aws/script.sh	13
deploy/jenkins/jenkins-jobs/deploy-dev-az/prepare-assets.sh	36
deploy/jenkins/jenkins-jobs/deploy-dev-az/run-pipectl.sh	60
deploy/jenkins/jenkins-jobs/deploy-dev-az/script.sh	13
deploy/jenkins/jenkins-sqs-trigger/poll_queue.sh	30
deploy/jenkins/restart-jenkins.sh	36
deploy/jenkins/run-jenkins.sh	66
deploy/pipectl/build-pipectl.sh	66
deploy/pipectl/pipectl-template.sh	44
deploy/repos/build-all.sh	22
deploy/repos/build-repo-deb.sh	128
deploy/repos/build-repo-pypi.sh	100
deploy/repos/build-repo-rpm.sh	99
deploy/repos/build-rocky-draft.sh	114
deploy/repos/custom-packages/pack-nvme-cli.sh	19
deploy/repos/download-scripts/rocky8/cloudfuse.sh	9
deploy/repos/download-scripts/rocky8/common.sh	18
deploy/repos/download-scripts/rocky8/dev.sh	9
deploy/repos/download-scripts/rocky8/dind.sh	9
deploy/repos/download-scripts/rocky8/lfs.sh	9
deploy/repos/download-scripts/rocky8/sge.sh	14
deploy/repos/download-scripts/rpm7/cloudfuse.sh	15
deploy/repos/download-scripts/rpm7/common.sh	19
deploy/repos/download-scripts/rpm7/dev.sh	10
deploy/repos/download-scripts/rpm7/dind.sh	12
deploy/repos/download-scripts/rpm7/lfs.sh	5
deploy/repos/download-scripts/rpm7/module.sh	7
deploy/repos/download-scripts/rpm7/nice.sh	14
deploy/repos/download-scripts/rpm7/sge.sh	19
deploy/repos/download-scripts/rpm8/cloudfuse.sh	18
deploy/repos/download-scripts/rpm8/common.sh	18
deploy/repos/download-scripts/rpm8/dev.sh	9
deploy/repos/download-scripts/rpm8/dind.sh	9
deploy/repos/download-scripts/rpm8/lfs.sh	7
deploy/repos/download-scripts/rpm8/sge.sh	14
deploy/travis/travis_pack_dist.sh	48
deploy/travis/travis_publish_docs.sh	24
docker-comp-scan/build.gradle	38
docker-comp-scan/configure_tmpfs.sh	7
docker-comp-scan/docker-comp-scan.sh	5
elasticsearch-agent/build.gradle	69
fs-browser/build.gradle	54
fs-browser/build.sh	31
fs-browser/fs-browser-client/build.gradle	35
fs-browser/fs-browser-client/config/webpack.config.js	347
git-reader/build.gradle	42
gradlew.bat	61
hcs-image-viewer/configuration/webpack/module.js	15
hcs-image-viewer/webpack.config.js	19
hcs-image-viewer/webpack.dev.config.js	18
jwt-generator/build.gradle	28
monitoring-service/build.gradle	54
notifier/build.gradle	1
notifier/notifier.sh	1
notifier/smtp/build.gradle	42
pipe-cli/build.gradle	164
pipe-cli/build_linux.sh	164
pipe-cli/build_mac.sh	114
pipe-cli/build_mac_arm.sh	84
pipe-cli/build_mac_py39.sh	79
pipe-cli/build_windows.sh	207
pipe-cli/gradlew.bat	66
pipe-cli/mount/build_mount.sh	48
pipe-cli/pipe.bat	29
pipe-cli/settings.gradle	1
scripts/autoscaling/emergency_node_terminator.sh	152
scripts/autoscaling/fsautoscale.sh	350
scripts/autoscaling/init_aws_native.sh	303
scripts/autoscaling/init_multicloud.sh	330
scripts/autoscaling/init_multicloud_v1.15.4.sh	492
scripts/commit-run-scripts/cleanup_container.sh	40
scripts/commit-run-scripts/commit_run.sh	82
scripts/commit-run-scripts/commit_run_starter.sh	62
scripts/commit-run-scripts/common_commit_initialization.sh	122
scripts/commit-run-scripts/container_layers_count.sh	7
scripts/commit-run-scripts/container_size.sh	1
scripts/commit-run-scripts/limit_bandwidth.sh	131
scripts/commit-run-scripts/pause_run.sh	136
scripts/commit-run-scripts/squash_docker_image.sh	96
scripts/docker-config/docker-login.sh	80
scripts/dts/deploy_dts.sh	149
scripts/dts/install_dts.sh	52
scripts/elasticsearch/update_run_billing.sh	17
scripts/elasticsearch/update_storage_billing.sh	17
scripts/git-role-management/syncgit_install.sh	13
scripts/nfs-roles-management/syncmounts.sh	240
scripts/pipeline-launch/init.sh	104
scripts/pipeline-launch/launch.sh	2035
scripts/pipeline-scripts/generate_components_versions.sh	11
scripts/pipeline-scripts/transfer_path.sh	25
settings.gradle	24
storage-lifecycle-service/build.gradle	42
vm-monitor/build.gradle	57
workflows/build.gradle	17
workflows/gpustat/build-linux.sh	72
workflows/pipe-demo/ngs/batch/src/batch.sh	22
workflows/pipe-demo/ngs/demultiplex/src/demultiplex.sh	85
workflows/pipe-demo/ngs/msgen/src/msgen.sh	304
workflows/pipe-demo/ngs/simple-variant-calling/src/variantcalling.sh	57
workflows/pipe-demo/ngs/wes-analysis/src/wes-analysis.sh	169
workflows/pipe-templates/__AWS_HEALTHOMICS/AWS-HealthOmics-Workflow/src/run-omics-workflow.sh	21
workflows/pipe-templates/__COMMON/shell/src/@.sh	1
workflows/pipe-templates/__SYSTEM/system_jobs/src/launch_system_job.sh	56