{"id":23442555,"url":"https://github.com/mvdoc/pycortex-singularity","last_synced_at":"2026-02-04T02:04:47.612Z","repository":{"id":75577354,"uuid":"121701265","full_name":"mvdoc/pycortex-singularity","owner":"mvdoc","description":"Singularity definition file for pycortex","archived":false,"fork":false,"pushed_at":"2018-02-16T18:41:12.000Z","size":5,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-09T21:49:35.002Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"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/mvdoc.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":"2018-02-16T00:45:53.000Z","updated_at":"2018-02-16T00:45:53.000Z","dependencies_parsed_at":"2023-06-06T23:30:37.031Z","dependency_job_id":null,"html_url":"https://github.com/mvdoc/pycortex-singularity","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mvdoc/pycortex-singularity","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fpycortex-singularity","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fpycortex-singularity/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fpycortex-singularity/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fpycortex-singularity/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mvdoc","download_url":"https://codeload.github.com/mvdoc/pycortex-singularity/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mvdoc%2Fpycortex-singularity/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264375692,"owners_count":23598427,"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":"2024-12-23T17:32:45.250Z","updated_at":"2026-02-04T02:04:47.560Z","avatar_url":"https://github.com/mvdoc.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":" [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/604)\n# pycortex Singularity container\n\nThis repository contains a singularity definition file to create a\ncontainer with [pycortex](https://gallantlab.github.io), FreeSurfer, and\nFSL. It installs the `glrework-merged` branch of pycortex. Pycortex's\nfilestore database needs to be mounted externally so that it is\npersistent, and must be pointed to `/cortex-filestore` inside the\ncontainer.\n\n## How to\n\n### 1. Build the container (this assumes Singularity \u003e= 2.4.2), or pull from singularity hub\n\n```terminal\nsingularity build pycortex.img Singularity\n```\n\nalternatively, the image can be pulled from singularity-hub\n\n```terminal\nsingularity pull --name pycortex.img shub://mvdoc/pycortex-singularity\n```\n\n### 2. Run it mounting the relevant directories, e.g.\n\n```terminal\nsingularity run -B /path/to/my/data:/data \\\n    -B /path/to/my/filestore:/cortex-filestore \\\n    -e -c pycortex.img\n```\n\nThis will start a shell inside the container; then one can run a jupyter\nnotebook session with\n\n```terminal\njupyter notebook --no-browser --port=9999\n```\n\nIf you need to use FreeSurfer, you should set the environment variable `FS_LICENSE` to point to your `license.txt` file:\n\n```terminal\nexport FS_LICENSE=/path/to/license.txt\n```\n\nThe container can also be used as a wrapper for commands, for example\n\n```terminal\n$ singularity run \\\n    -B /path/to/my/filestore:/cortex-filestore \\\n    -e -c pycortex.img \\\n    \"python -c 'import cortex; print(cortex.__file__)'\"\n\n/src/pycortex/cortex/__init__.py\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmvdoc%2Fpycortex-singularity","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmvdoc%2Fpycortex-singularity","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmvdoc%2Fpycortex-singularity/lists"}