{"id":43894414,"url":"https://github.com/recursionpharma/bc_code","last_synced_at":"2026-02-06T17:14:52.403Z","repository":{"id":193365973,"uuid":"688623218","full_name":"recursionpharma/bc_code","owner":"recursionpharma","description":"Code Server Interactive App for BioHive Portal (Open OnDemand)","archived":false,"fork":false,"pushed_at":"2025-06-05T18:09:10.000Z","size":129,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"trunk","last_synced_at":"2025-06-05T19:21:58.747Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/recursionpharma.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-09-07T18:34:22.000Z","updated_at":"2025-06-05T18:09:13.000Z","dependencies_parsed_at":"2025-01-15T00:24:25.637Z","dependency_job_id":"28514305-36ed-4e0b-ab73-e433584e57fc","html_url":"https://github.com/recursionpharma/bc_code","commit_stats":null,"previous_names":["recursionpharma/bc_code"],"tags_count":0,"template":false,"template_full_name":"recursionpharma/bc_jupyter","purl":"pkg:github/recursionpharma/bc_code","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/recursionpharma%2Fbc_code","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/recursionpharma%2Fbc_code/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/recursionpharma%2Fbc_code/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/recursionpharma%2Fbc_code/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/recursionpharma","download_url":"https://codeload.github.com/recursionpharma/bc_code/tar.gz/refs/heads/trunk","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/recursionpharma%2Fbc_code/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29169403,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T16:33:35.550Z","status":"ssl_error","status_checked_at":"2026-02-06T16:33:30.716Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-02-06T17:14:51.744Z","updated_at":"2026-02-06T17:14:52.398Z","avatar_url":"https://github.com/recursionpharma.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![scorecard-score](https://github.com/recursionpharma/octo-guard-badges/blob/trunk/badges/repo/bc_code/maturity_score.svg?raw=true)](https://infosec-docs.prod.rxrx.io/octoguard/scorecards/bc_code)\n[![scorecard-status](https://github.com/recursionpharma/octo-guard-badges/blob/trunk/badges/repo/bc_code/scorecard_status.svg?raw=true)](https://infosec-docs.prod.rxrx.io/octoguard/scorecards/bc_code)\n[![team-status](https://github.com/recursionpharma/octo-guard-badges/blob/trunk/badges/team/information-technology/team_status.svg?raw=true)](https://infosec-docs.prod.rxrx.io/octoguard/team-reports/information-technology)\n# Batch Connect - OSC Code Server\n\n![GitHub Release](https://img.shields.io/github/release/osc/bc_osc_codeserver.svg)\n[![GitHub License](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/licenses/MIT)\n\nAn improved file viewer / editor for OSC OnDemand that launches a\nCode Server within an Owens batch job. Code Server leverages VSCode as its\neditor.\n\n## Prerequisites\n\nThis Batch Connect app requires the following software be installed on the\n**compute nodes** that the batch job is intended to run on (**NOT** the\nOnDemand node):\n\n- [Lmod] 6.0.1+ or any other `module purge` and `module load \u003cmodules\u003e` based\n  CLI used to load appropriate environments within the batch job before\n  launching Code server.\n- [Code Server] 2.x+ available from Github: https://github.com/cdr/code-server/releases\n\n[Code Server]: https://coder.com/\n[Lmod]: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod\n[VS Code]: https://code.visualstudio.com/\n\n## Install\n\n1. Use Git to clone this app and checkout the desired branch/version you want to\nuse and place this wherever you store batch connect apps (`/var/www/ood/apps/sys` or `~/ondemand/dev`):\n\n    ```sh\n    scl enable git29 -- git clone \u003crepo\u003e\n    cd \u003cdir\u003e\n    scl enable git29 -- git checkout \u003ctag/branch\u003e\n    ```\n\n2. Deploy code-server on your systems.\n\n    ```sh\n    # replace URL with latest release from code-server\n    wget https://github.com/cdr/code-server/releases/download/3.2.0/code-server-3.2.0-linux-x86_64.tar.gz\n    tar -xzf code-server-3.2.0-linux-x86_64.tar.gz\n    ```\n    \n3. You will notice code-server is an executable inside that directory and can get the full path: \n    \n    ```sh\n    $ readlink -f code-server-3.2.0-linux-x86_64.tar.gz\n    /users/PZS0562/efranz/code-server-3.2.0-linux-x86_64.tar.gz\n    ```\n\n4. Update the path to the code-server binary in the script https://github.com/OSC/bc_osc_codeserver/blob/3082790ee69c82fe6fe757074da7d8d18c7d7e3d/template/script.sh.erb#L27:\n\n    ```diff\n     # An arbitrary path...\n    - /fs/project/PZS0714/mrodgers/bin/code-server-2.1523-vsc1.38.1 \\\n    + /users/PZS0562/efranz/code-server-3.2.0-linux-x86_64/code-server \\\n     --auth=password \\\n     --port=\"$port\" \\\n    ```\n\n5. Update form.yml to use the correct cluster, and any other changes as necessary to form.yml or submit.yml that is appropriate for your cluster.\n\n## Update\n\nTo update the app you would:\n\n```sh\ncd \u003cdir\u003e\nscl enable git29 -- git fetch\nscl enable git29 -- git checkout \u003ctag/branch\u003e\n```\n\nAgain, you do not need to restart the app as it isn't a Passenger app.\n\n## Known Issues\n\n- In-app installation of extensions does not work\n- The authentication provided by code-server is unencrypted\n\n## Contributing\n\n1. Fork it ( https://github.com/OSC/bc_osc_codeserver/fork )\n2. Create your feature branch (`git checkout -b my-new-feature`)\n3. Commit your changes (`git commit -am 'Add some feature'`)\n4. Push to the branch (`git push origin my-new-feature`)\n5. Create a new Pull Request\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frecursionpharma%2Fbc_code","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frecursionpharma%2Fbc_code","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frecursionpharma%2Fbc_code/lists"}