https://github.com/billdenney/pharmacometrics-docker

Dockerfiles for pharmacometrics-related software: NONMEM and Perl-speaks-NONMEM
https://github.com/billdenney/pharmacometrics-docker

dockerfile nonmem psn

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Dockerfiles for pharmacometrics-related software: NONMEM and Perl-speaks-NONMEM

• Host: GitHub
• URL: https://github.com/billdenney/pharmacometrics-docker
• Owner: billdenney
• Created: 2016-05-24T13:46:42.000Z (over 8 years ago)
• Default Branch: main
• Last Pushed: 2022-09-09T18:31:46.000Z (about 2 years ago)
• Last Synced: 2023-02-27T13:47:14.767Z (over 1 year ago)
• Topics: dockerfile, nonmem, psn
• Language: Dockerfile
• Homepage:
• Size: 60.5 KB
• Stars: 16
• Watchers: 5
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Pharmacometrics-Docker

Dockerfiles for pharmacometrics-related software: NONMEM and

Perl-speaks-NONMEM

Each of these files is intended to help improve reproducible research

by enabling the use of Docker images to keep all requirements for

execution in a single container.

## NONMEM

A dockerfile to build a gfortran-run NONMEM installation.  It will

require a NONMEM license file (in the same directory, named

`nonmem.lic`).  See the instructions in the comments of the file for

how to speed up the run (and minimize download time).

http://www.iconplc.com/innovation/solutions/nonmem/

Due to NONMEM requirements, NONMEM versions older than 7.5.1 will not

work with Ubuntu versions after 20.04.

### Installation

* Copy your nonmem license file (named `nonmen.lic` to the same

  directory as the Dockerfile.

* Have your NONMEM zip file password handy

* See the instructions in the top of the Dockerfile for the command

  to run.

* For NONMEM, automatic download from Icon may be unreliable

  (https://github.com/billdenney/Pharmacometrics-Docker/issues/2).

  Manual download and serving the file from a local webserver is

  recommended.  (See the top of the Dockerfile for instructions.)

### Running

It is recommended to run NONMEM via Perl-speaks-NONMEM (below).  To

run NONMEM directly, you can run the following command:

    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

### Updating Your License

To update your license file without requiring a rebuild of the Docker

image, you can mount a directory containing the license file in the

/license directory of your image (note the first -v argument):

    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

## Perl-speaks-NONMEM

A dockerfile to build a Perl-speaks-NONMEM (PsN) installation on top

of the NONMEM docker image.  You must build the NONMEM image first to

build the PsN image.

https://github.com/UUPharmacometrics/PsN/

### Installation

* Install the NONMEM image above (this image starts from that image)

* See the instructions in the top of the Dockerfile for the command

  to run.

### Running

It is recommended to run NONMEM via the dockpsn script.  To run the

dockpsn command, set it up by copying it to a location in the path:

    cp scripts/dockpsn /usr/local/bin/dockpsn

Then you can use it by running it followed by the PsN command of

interest:

    dockpsn execute CONTROL.mod

To run PsN directly, you can use the following command (substitute

`execute` for the PsN command of interest):

    docker run --rm --user=$(id -u):$(id -g) -v $(pwd):/data -w /data humanpredictions/psn execute CONTROL.mod

### Updating Your License

If you use the `dockpsn` command, it will look for an updated license

in the `/opt/NONMEM/license` directory by default.  If none is found

there, it will run with the license used when the image was created.

To update your license file without requiring a rebuild of the Docker

image, you can mount a directory containing the license file in the

/license directory of your image (note the first -v argument):

    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

That is automatically done with the `dockpsn` command.