{"id":18321868,"url":"https://github.com/sorgerlab/cycif-benchmarking-docker-ashlar","last_synced_at":"2026-05-09T19:42:46.460Z","repository":{"id":138588212,"uuid":"129132066","full_name":"sorgerlab/cycif-benchmarking-docker-ashlar","owner":"sorgerlab","description":"Docker build for benchmarking ASHLAR for AWS Batch","archived":false,"fork":false,"pushed_at":"2018-04-17T17:46:47.000Z","size":4,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-02-15T08:34:58.265Z","etag":null,"topics":["aws","benchmarking","cycif","docker"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sorgerlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2018-04-11T17:44:22.000Z","updated_at":"2024-03-12T12:43:08.000Z","dependencies_parsed_at":null,"dependency_job_id":"f7d82d56-00c9-4220-9999-d1e2ea5b3aaf","html_url":"https://github.com/sorgerlab/cycif-benchmarking-docker-ashlar","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sorgerlab%2Fcycif-benchmarking-docker-ashlar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sorgerlab%2Fcycif-benchmarking-docker-ashlar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sorgerlab%2Fcycif-benchmarking-docker-ashlar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sorgerlab%2Fcycif-benchmarking-docker-ashlar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sorgerlab","download_url":"https://codeload.github.com/sorgerlab/cycif-benchmarking-docker-ashlar/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248055275,"owners_count":21040151,"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":["aws","benchmarking","cycif","docker"],"created_at":"2024-11-05T18:22:11.582Z","updated_at":"2026-05-09T19:42:41.417Z","avatar_url":"https://github.com/sorgerlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CycIF Benchmarking - ASHLAR\n\nThis Docker image is designed for use within AWS BATCH.\n\n## Job configuration YAML\n\nA YAML file containing the configuration for a job must be provided to the\ncontainer. Each configuration has the form:\n\n```yaml\ninputs:\n  - s3://example/dataset1/raw/cycle1.rcpnl\n  - s3://example/dataset1/raw/cycle2.rcpnl\noutput: s3://example/dataset1/ashlar/\narguments:\n  - /mnt/input/*.rcpnl\n```\n\nAll `inputs` are copied into the `/mnt/input` directory in the Docker container.\nIf an input is suffixed with a `/` it is recursively copied to `/mnt/input` so\nthat the relative directory structure is maintained.\n\n`arguments` is passed directly to `ashlar` so a series of options can be\nspecified as a list. No default is provided to `ashlar` for the required\n`filepaths` positional argument so this must be specified.\n\nThis configuration file's location in S3 is passed to the docker container as\nthe only argument or can alternatively be passed as a string in the environment\nvariable `CONFIG`.\n\n## Local usage\n\nThis image can be used locally as long as appropriate environment variables\nare set when instantiating the docker container.\n\n```bash\n# Passing the configuration file's location in S3\ndocker run \\\n  -e AWS_SECRET_ACCESS_KEY=\"${AWS_SECRET_ACCESS_KEY}\" \\\n  -e AWS_ACCESS_KEY_ID=\"${AWS_ACCESS_KEY_ID}\" \\\n  -e AWS_SESSION_TOKEN=\"${AWS_SESSION_TOKEN}\" \\\n  cycif-benchmarking-ashlar:latest \\\n  s3://example/config.yml\n\n# Passing the configuration as an environment variable\ndocker run \\\n  -e AWS_SECRET_ACCESS_KEY=\"${AWS_SECRET_ACCESS_KEY}\" \\\n  -e AWS_ACCESS_KEY_ID=\"${AWS_ACCESS_KEY_ID}\" \\\n  -e AWS_SESSION_TOKEN=\"${AWS_SESSION_TOKEN}\" \\\n  -e \"CONFIG=$(\u003cconfig.yml)\" \\\n  cycif-benchmarking-ashlar:latest\n```\n\nIt is recommended to use a session token inside the Docker container, which can\nbe generated using the AWS CLI.\n\n```bash\naws sts get-session-token\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsorgerlab%2Fcycif-benchmarking-docker-ashlar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsorgerlab%2Fcycif-benchmarking-docker-ashlar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsorgerlab%2Fcycif-benchmarking-docker-ashlar/lists"}