Docker-related procedures

In this section, we will show you a few things related specifically to running code reproducibly with Docker. For more general debugging tips for Docker and other computer languages, see our wiki.

(coming soon)

Checklist

• If running licensed software (e.g. MATLAB, Stata), know where the license is stored. If you do not, you cannot run the relevant Docker image.

• Docker (or equivalent) is installed

• The replication package’s main directory will be mounted into the Docker container. The precise location will depend on the Docker image. Know where it is.

Windows

Note

Docker does not run on CCSS Cloud! These instructions may work on a personal laptop.

See Docker on Windows.

Mac/generic Linux

Note

Mac-specific: In addition to the default Docker client, OrbStack can be used for personal use. We have found it to have less of a computational burden.

BioHPC

Note

BioHPC procedures differ somewhat. Wherever it says docker, docker1 must be replaced. Read the Quickstart for other things. Where relevant, we will point out differences below.

• Ensure you are either connected to the campus network directly or through a VPN. You cannot connect to the compute node without being on campus or connected via VPN. See instruction for CU VPN setup.

• Login to BioHPC through this link. If do not have an account yet, follow instructions at Linux Remote

• Reserve a node

• Access the node

• Launch a terminal and change your directory to /home2/ecco_lv39/Workspace. Do not work on the home directory which has your NetID. Type pwd to check your current directory.

• Clone your repository into this directory aeagit-###.

If there is no Docker folder

• Create a folder Docker in the same directory as your repository.

• Create a Dockerfile. A simple example might be (here, to install Ox)

# syntax=docker/dockerfile:1.2
# First stage
FROM ubuntu:22.04 
ENV VERSION 9
ENV SUBVERSION 10
ENV MINORVERSION 0

RUN apt-get update \
    && DEBIAN_FRONTEND=noninteractive apt-get upgrade -y  \
    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
         locales \
         libncurses5 \
         libfontconfig1 \
         git \
         nano \
         unzip \
         wget \
    && rm -rf /var/lib/apt/lists/* \
    && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8

# Set a few more things
ENV LANG en_US.utf8

# Adding Ox
RUN wget -O oxconsole.deb https://www.doornik.com/download/oxmetrics${VERSION}/Ox_Console/oxconsole_${VERSION}.${SUBVERSION}-${MINORVERSION}_amd64.deb \
    && apt-get install ./oxconsole.deb

• You might also find a build.sh script useful:

#!/bin/bash

[[ -z $1 ]] && TAG=$(date +%F) || TAG=$1
MYHUBID=aeadataeditor
MYIMG=aearep-XXXX

DOCKER_BUILDKIT=1 docker1 build   -t ${MYIMG}:$TAG $(pwd)/

• Make this file executable: chmod +x build.sh

• Go back to your repository directory (cd ..)

• git add Docker and push.

If there is a Docker folder

• Change the directory to your Docker folder and build the image ./build.sh. Check completion by docker1 images.

• Once the image is built, go to the directory where you want to run your container. Type

docker1 run -it --rm -v "$(pwd)":/project -w /project biohpc_lv39/aearep-###:TAG

(modify repository number and TAG as needed).

• In the bash shell inside the Docker container, run any command lines as identified by the authors.

Run the code