How to save data from a docker container on a local host? - docker

Question

I run R-Studio in a container on GitLab. R-Studio build a lot of csv and pdf files. When I run
docker run --rm -it registry.gitlab.com/user/paperboy /bin/bash
I can find in the folder /home/output/csv and /home/output/pdf the files. I will save all this files in a /output/csv and /output/pdf files on a host, in my case on GitLab. The question is how to save data outside the docker Container?
Here is my Dockerfile.
FROM rocker/r-base:latest
RUN apt-get update \
&& apt-get install -yq --no-install-recommends groff \
&& rm -rf /var/lib/apt/lists/*
# Create directories
RUN mkdir -p /home/output/ /home/output/csv/ /home/output/pdf/ /home/script/
WORKDIR /home/script
# Install R-packages
COPY /src/install_packages.R /home/script/install_packages.R
RUN Rscript /home/script/install_packages.R
# Copy data
COPY /src/pairs.csv /home/script/pairs.csv
COPY /src/master.R /home/script/master.R
COPY /src/paperboy.ms /home/script/paperboy.ms
# Run the script
RUN ["Rscript", "master.R"]
$ docker run -d
-v $(pwd)/output/:/home/output
-v $(pwd)/output/csv/:/home/output/csv
-v $(pwd)/output/pdf/:/home/output/pdf
$CONTAINER_IMAGE/$DOCKER_IMAGE
5d11eb7e3d93e8b98b6381f1970c25be426ff67abef5e378b715263f174849c9
This is a part from the .gitlab-ci.yml
run:
stage: run
script:
- git remote set-url origin https://$GIT_CI_USER:$GIT_CI_PASS#gitlab.com/$CI_PROJECT_PATH.git
- git config --global user.name ""
- git config --global user.email ""
- git checkout
- docker login registry.gitlab.com --username gitlab+deploy-token-aaaa --password bbbb
- docker pull $CONTAINER_IMAGE/$DOCKER_IMAGE
- docker image ls
- docker run -t -d
-v $(pwd)/output/:/home/output
-v $(pwd)/user/paperboy/output/csv/:/home/output/csv
-v $(pwd)/user/paperboy/output/pdf/:/home/output/pdf
$CONTAINER_IMAGE/$DOCKER_IMAGE
- rm -rf "%CACHE_PATH%/%CI_PIPELINE_ID%"
- pwd
- ls -la
- ls -laR output
- git status
only:
- master
The csv and pdf folder are empty.
$ ls -laR output
output:
total 32
drwxr-xr-x 4 root root 4096 Oct 8 11:37 .
drwxrwxrwx 5 root root 4096 Oct 8 11:37 ..
drwxr-xr-x 2 root root 4096 Oct 8 11:37 csv
drwxr-xr-x 2 root root 4096 Oct 8 11:37 pdf
output/csv:
total 16
drwxr-xr-x 2 root root 4096 Oct 8 11:37 .
drwxr-xr-x 4 root root 4096 Oct 8 11:37 ..
output/pdf:
total 16
drwxr-xr-x 2 root root 4096 Oct 8 11:37 .
drwxr-xr-x 4 root root 4096 Oct 8 11:37 ..