{"id":19749619,"url":"https://github.com/mskcc/hermes","last_synced_at":"2025-04-30T09:31:26.550Z","repository":{"id":38985266,"uuid":"243080492","full_name":"mskcc/hermes","owner":"mskcc","description":"Data collection management and analysis of information","archived":false,"fork":false,"pushed_at":"2023-03-07T18:47:30.000Z","size":6420,"stargazers_count":4,"open_issues_count":67,"forks_count":1,"subscribers_count":11,"default_branch":"develop","last_synced_at":"2023-08-06T05:35:14.729Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","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":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-02-25T19:10:17.000Z","updated_at":"2023-06-05T02:46:12.000Z","dependencies_parsed_at":"2023-02-15T05:01:33.146Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/hermes","commit_stats":null,"previous_names":[],"tags_count":2,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fhermes","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fhermes/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fhermes/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Fhermes/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/hermes/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224205119,"owners_count":17273256,"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":"2024-11-12T02:27:29.049Z","updated_at":"2024-11-12T02:27:29.498Z","avatar_url":"https://github.com/mskcc.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Seqosystem\nTODO Description\n\n## Dependencies\nTested with the following versions.\n* [Elixir 1.10.4](https://elixir-lang.org/)\n* PostgreSQL 12.1\n* Node 14.5.x\n\n## Code Layout\n```\napps/\n├── dashboard/ - Primary point of entry, an instance of [Phoenix Web framework](https://www.phoenixframework.org/)\n├── lims_client/ - Configurable library for making requests to a LIMS server that can return JSON.\n└── beagle_client/ - Configurable library for making requests to Beagle, MSK's interface for [Toil](https://github.com/DataBiosphere/toil) orchestration.\n```\n\n## Configuration (TODO)\n## Development (TODO)\n1. Install [Docker](https://docs.docker.com/compose/install/).\n2. `docker-compose up`\n3. (Optional) If you plan to do releases, be sure to copy your pub key to `.ssh/authorized_keys` on deploy@\u003caccess01|access02\u003e\n4. run `mix phx.gen.cert` to generate the self-signed ssl certificates\n\n## Deployment (VM)\n### Release (causes downtime)\n```\nmix edeliver build release\n# To release a specific branch: mix edeliver build release --branch=\"\u003cbranch_name\u003e\"\nmix edeliver deploy release to staging\nmix edeliver start staging\nOR (will run the above) mix edeliver update staging --start-deploy --branch=\"\u003cbranch_name\u003e\"\n```\n\n### Release by Upgrade (Use this, this should not cause downtime)\n```\nmix edeliver upgrade staging\nmix edeliver upgrade production\n\n```\n### Migrate\nNot ready, see https://github.com/edeliver/edeliver/issues/235\n```\nmix edeliver migrate staging\n```\ninstead do the following for now...\n```\nssh deploy@\u003cserver\u003e\n./seqosystem/bin/seqosystem rpc 'Dashboard.Release.migrate'\n```\n\n### Setting-up a Machine\n```\n# As root, install packages\nwget https://packages.erlang-solutions.com/erlang/rpm/centos/7/x86_64/esl-erlang_23.0.2-2~centos~7_amd64.rpm\nwget https://packages.erlang-solutions.com/erlang/rpm/centos/7/x86_64/elixir_1.10.4-1~centos~7_all.rpm\nyum remove erlang*\nyum remove nodejs*\nyum localinstall esl-erlang_23.0.2-2~centos~7_amd64.rpm\nyum localinstall elixir_1.10.4-1~centos~7_all.rpm\ncurl -sL https://rpm.nodesource.com/setup_14.x | sudo bash -\nyum install -y nodejs\nyum install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm\nyum install postgresql11-server\n\nvim /etc/ssh/sshd_config\n# Append `deploy` to `AllowGroups` (if server is sep-up with Puppet, may require Server Admin assistance)\n\n# Set-up a Deploy user\nuseradd deploy\nsu deploy\nmkdir .ssh\nvim .ssh/authorized_keys\necho \"github.com ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==\" \u003e\u003e ~/.ssh/known_hosts\n# Copy your local pub key\nexit # Back as root\n\nservice sshd restart\n# Ensure you can ssh in as yourself and as `deploy@\u003cserver\u003e`. Do not disconnect if not, if sshd is running you can see what's wrong in `/var/log/secure`\n\n# Copy over the config.\nscp config/prod.secret.exs deploy@access01:/home/deploy\n\n# Install PostgreSQL\n/usr/pgsql-11/bin/postgresql-11-setup initdb\nsystemctl start postgresql-11\nsystemctl enable postgresql-11\n\nsu - postgres\nvim /var/lib/pgsql/11/data/pg_hba.conf # Change \"IPv4 local connections\" METHOD to md5\ncreatedb \u003cDB_NAME\u003e\ncreateuser \u003cUSERNAME\u003e --interactive\npsql #ALTER USER caesar WITH password '\u003cPASSWORD\u003e';\n# As deploy, make sure the database url is set in the ENVAR\n\nexit\n# As root\nservice postgresql-11.service restart\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fhermes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fhermes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fhermes/lists"}