{"id":19749592,"url":"https://github.com/mskcc/roslin-core","last_synced_at":"2025-02-28T00:41:42.109Z","repository":{"id":72596969,"uuid":"114149986","full_name":"mskcc/roslin-core","owner":"mskcc","description":"Core of the Roslin pipeline","archived":false,"fork":false,"pushed_at":"2020-02-25T20:53:00.000Z","size":671,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":38,"default_branch":"2.1.x","last_synced_at":"2025-01-10T21:22:11.337Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mskcc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-12-13T17:32:35.000Z","updated_at":"2019-12-13T15:28:34.000Z","dependencies_parsed_at":"2023-06-19T14:36:45.981Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/roslin-core","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-core","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-core/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-core/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-core/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/roslin-core/tar.gz/refs/heads/2.1.x","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241079795,"owners_count":19906126,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-12T02:27:21.194Z","updated_at":"2025-02-28T00:41:42.103Z","avatar_url":"https://github.com/mskcc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Roslin-core\n\n\u003e Roslin-core handles submission, tracking, killing and restarting of projects through a roslin pipeline\n\n## Usage Guide\n\n## Tracking\n\nAll projects are automatically tracked on the mongo database specified in the core config. You can disable this by setting the ```ROSLIN_MONGO_DISABLE``` environment variable\n\n```\nexport ROSLIN_MONGO_DISABLE=\"True\"\n```\n\n### Submit a project\n\nUse the script `roslin_submit.py` to submit projects\n\n#### Arguments\n\n```\nusage: roslin_submit.py [-h] --name {variant} --version {2.5.0} --id\n                        PROJECT_ID --inputs INPUTS_YAML --workflow\n                        {Alignment,CdnaContam,GatherMetrics,GenerateQc,GenerateQcSV,MafProcessing,PairWorkflow,PairWorkflowSV,Realignment,SampleWorkflow,StructuralVariants,VariantCalling,VariantWorkflow,VariantWorkflowSV}\n                        --batch-system\n                        {LSF,Mesos,Torque,Slurm,HTCondor,singleMachine,parasol,gridEngine}\n                        [--cwl-batch-system {LSF,Mesos,Torque,Slurm,HTCondor,singleMachine,parasol,gridEngine}]\n                        [--debug] [--path PROJECT_PATH] [--test-mode]\n                        [--force-overwrite-results] [--on-start ON_START]\n                        [--on-complete ON_COMPLETE] [--on-fail ON_FAIL]\n                        [--on-success ON_SUCCESS] [--use-docker]\n                        [--docker-registry DOCKER_REGISTRY]\n                        [--foreground-mode] [--results RESULTS_DIR]\n                        [--max-mem MAX_MEM] [--max-cpu MAX_CPU]\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --name {variant}      Pipeline name (default: None)\n  --version {2.5.0}     Pipeline versions: (default: None)\n  --id PROJECT_ID       Project ID (e.g. Proj_5088_B) (default: None)\n  --inputs INPUTS_YAML  The path to your input yaml file ( required on non-\n                        restart runs ) (default: None)\n  --workflow {Alignment,CdnaContam,GatherMetrics,GenerateQc,GenerateQcSV,MafProcessing,PairWorkflow,PairWorkflowSV,Realignment,SampleWorkflow,StructuralVariants,VariantCalling,VariantWorkflow,VariantWorkflowSV}\n                        Workflow name ( required on non-restart runs )\n                        (default: None)\n  --batch-system {LSF,Mesos,Torque,Slurm,HTCondor,singleMachine,parasol,gridEngine}\n                        The batch system to submit the job (default: None)\n  --cwl-batch-system {LSF,Mesos,Torque,Slurm,HTCondor,singleMachine,parasol,gridEngine}\n                        The batch system to submit the cwl jobs (uses --batch-\n                        system if not set) (default: None)\n  --debug               Run the runner in debug mode (default: False)\n  --path PROJECT_PATH   Path to Project files (to store in database) (default:\n                        None)\n  --test-mode           Run the runner in test mode (default: False)\n  --force-overwrite-results\n                        Force overwrite if results folder already exists\n                        (default: False)\n  --on-start ON_START   Python script to run when the workflow starts\n                        (default: None)\n  --on-complete ON_COMPLETE\n                        Python script to run when the workflow completes\n                        (either fail or succeed) (default: None)\n  --on-fail ON_FAIL     Python script to run when the workflow fails (default:\n                        None)\n  --on-success ON_SUCCESS\n                        Python script to run when the workflow succeeds\n                        (default: None)\n  --use-docker          Use Docker instead of singularity (default: False)\n  --docker-registry DOCKER_REGISTRY\n                        Dockerhub registry to pull ( invoked only with --use-\n                        docker) (default: None)\n  --foreground-mode     Runs the pipeline the the foreground (default: False)\n  --results RESULTS_DIR\n                        Path to the directory to store results (default: None)\n  --max-mem MAX_MEM     The maximum amount of memory to request in GB (e.g.\n                        8G) (default: None)\n  --max-cpu MAX_CPU     The maximum amount of cpu to request (default: None)\n```\n\n### Kill a project\n\nUse the script `roslin_kill_project.py` to kill projects\n\n#### Arguments\n\n```\nusage: roslin_kill_project.py [-h] --name PIPELINE_NAME --version\n                              PIPELINE_VERSION --id PROJECT_ID --uuid\n                              PROJECT_UUID [--forceful]\n\nroslin kill project\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --name PIPELINE_NAME  Pipeline name (e.g. variant)\n  --version PIPELINE_VERSION\n                        Pipeline version (e.g. 2.4.0)\n  --id PROJECT_ID       Project ID (e.g. Proj_5088_B)\n  --uuid PROJECT_UUID   The uuid of the project\n  --forceful            Forcefully kill the project\n ```\n\n ### Restart a project\n\n Use the script `roslin_restart.py` to restart a project\n\n #### Arguments\n ```\nusage: roslin_restart.py [-h] --name {variant} --version {2.5.0.RC1} --id\n                         PROJECT_ID --restart RESTART_JOB_UUID\n                         [--foreground-mode]\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --name {variant}      Pipeline name (default: None)\n  --version {2.5.0.RC1}\n                        Pipeline versions: (default: None)\n  --id PROJECT_ID       Project ID (e.g. Proj_5088_B) (default: None)\n  --restart RESTART_JOB_UUID\n                        project uuid for restart (default: None)\n  --foreground-mode     Runs the pipeline the the foreground (default: False)\n  ```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Froslin-core","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Froslin-core","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Froslin-core/lists"}