{"id":17295496,"url":"https://github.com/billdenney/pharmacometrics-docker","last_synced_at":"2025-06-17T22:04:08.678Z","repository":{"id":56508879,"uuid":"59576974","full_name":"billdenney/Pharmacometrics-Docker","owner":"billdenney","description":"Dockerfiles for pharmacometrics-related software: NONMEM and Perl-speaks-NONMEM","archived":false,"fork":false,"pushed_at":"2022-09-09T18:31:46.000Z","size":62,"stargazers_count":18,"open_issues_count":1,"forks_count":2,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-04-13T03:20:54.524Z","etag":null,"topics":["dockerfile","nonmem","psn"],"latest_commit_sha":null,"homepage":"","language":"Dockerfile","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/billdenney.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}},"created_at":"2016-05-24T13:46:42.000Z","updated_at":"2024-06-06T11:47:49.000Z","dependencies_parsed_at":"2022-08-15T20:01:05.237Z","dependency_job_id":null,"html_url":"https://github.com/billdenney/Pharmacometrics-Docker","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/billdenney/Pharmacometrics-Docker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/billdenney%2FPharmacometrics-Docker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/billdenney%2FPharmacometrics-Docker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/billdenney%2FPharmacometrics-Docker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/billdenney%2FPharmacometrics-Docker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/billdenney","download_url":"https://codeload.github.com/billdenney/Pharmacometrics-Docker/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/billdenney%2FPharmacometrics-Docker/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260447652,"owners_count":23010542,"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":["dockerfile","nonmem","psn"],"created_at":"2024-10-15T11:10:28.359Z","updated_at":"2025-06-17T22:04:03.666Z","avatar_url":"https://github.com/billdenney.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Pharmacometrics-Docker\n\nDockerfiles for pharmacometrics-related software: NONMEM and\nPerl-speaks-NONMEM\n\nEach of these files is intended to help improve reproducible research\nby enabling the use of Docker images to keep all requirements for\nexecution in a single container.\n\n## NONMEM\n\nA dockerfile to build a gfortran-run NONMEM installation.  It will\nrequire a NONMEM license file (in the same directory, named\n`nonmem.lic`).  See the instructions in the comments of the file for\nhow to speed up the run (and minimize download time).\n\nhttp://www.iconplc.com/innovation/solutions/nonmem/\n\nDue to NONMEM requirements, NONMEM versions older than 7.5.1 will not\nwork with Ubuntu versions after 20.04.\n\n### Installation\n\n* Copy your nonmem license file (named `nonmen.lic` to the same\n  directory as the Dockerfile.\n* Have your NONMEM zip file password handy\n* See the instructions in the top of the Dockerfile for the command\n  to run.\n* For NONMEM, automatic download from Icon may be unreliable\n  (https://github.com/billdenney/Pharmacometrics-Docker/issues/2).\n  Manual download and serving the file from a local webserver is\n  recommended.  (See the top of the Dockerfile for instructions.)\n\n### Running\n\nIt is recommended to run NONMEM via Perl-speaks-NONMEM (below).  To\nrun NONMEM directly, you can run the following command:\n\n    docker run --rm --user=$(id -u):$(id -g) -v $(pwd):/data -w /data humanpredictions/nonmem /opt/NONMEM/nm_current/run/nmfe CONTROL.mod CONTROL.res\n\n### Updating Your License\n\nTo update your license file without requiring a rebuild of the Docker\nimage, you can mount a directory containing the license file in the\n/license directory of your image (note the first -v argument):\n\n    docker run --rm --user=$(id -u):$(id -g) -v /opt/NONMEM/license:/opt/NONMEM/nm_current/license -v $(pwd):/data -w /data humanpredictions/nonmem /opt/NONMEM/nm_current/run/nmfe CONTROL.mod CONTROL.res\n\n## Perl-speaks-NONMEM\n\nA dockerfile to build a Perl-speaks-NONMEM (PsN) installation on top\nof the NONMEM docker image.  You must build the NONMEM image first to\nbuild the PsN image.\n\nhttps://github.com/UUPharmacometrics/PsN/\n\n### Installation\n\n* Install the NONMEM image above (this image starts from that image)\n* See the instructions in the top of the Dockerfile for the command\n  to run.\n\n### Running\n\nIt is recommended to run NONMEM via the dockpsn script.  To run the\ndockpsn command, set it up by copying it to a location in the path:\n\n    cp scripts/dockpsn /usr/local/bin/dockpsn\n\nThen you can use it by running it followed by the PsN command of\ninterest:\n\n    dockpsn execute CONTROL.mod\n\nTo run PsN directly, you can use the following command (substitute\n`execute` for the PsN command of interest):\n\n    docker run --rm --user=$(id -u):$(id -g) -v $(pwd):/data -w /data humanpredictions/psn execute CONTROL.mod\n\n### Updating Your License\n\nIf you use the `dockpsn` command, it will look for an updated license\nin the `/opt/NONMEM/license` directory by default.  If none is found\nthere, it will run with the license used when the image was created.\n\nTo update your license file without requiring a rebuild of the Docker\nimage, you can mount a directory containing the license file in the\n/license directory of your image (note the first -v argument):\n\n    docker run --rm --user=$(id -u):$(id -g) -v /opt/NONMEM/license:/opt/NONMEM/nm_current/license -v $(pwd):/data -w /data humanpredictions/psn execute CONTROL.mod\n\nThat is automatically done with the `dockpsn` command.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbilldenney%2Fpharmacometrics-docker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbilldenney%2Fpharmacometrics-docker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbilldenney%2Fpharmacometrics-docker/lists"}