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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

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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.