I am able to set up a Dockerfile with default ENV variables that I can then configure when running my docker container, e.g. in a Dockerfile I have the lines:
ENV USERNAME ropensci
ENV EMAIL ropensci#github.com
RUN git config --global user.name $USERNAME
RUN git config --global user.email $EMAIL
Great. When I launch an interactive session:
docker run -it --env USERNAME="Carl" --env EMAIL=cboettig#example.com myimage /bin/bash
I can then issue the command git config --list and see that git is configured to use the values I provided on the command line instead of the defaults.
However, my Dockerfile is also configured to run an RStudio server that I can then log into in the browser when running the image in Daemon mode:
docker run -d -p 8787:8787 --env USERNAME="Carl" --env EMAIL=cboettig#example.com cboettig/ropensci-docker
I go to localhost:8787 and log in to RStudio which all works as expected, start a new "Project" with git enabled, but then RStudio cannot find my git name & email. I can open the shell from the RStudio menu and run git config --list or echo $USERNAME and I just get a blank value. Why does this work for /bin/bash but not from RStudio and how do I fix it?
Your git config is set on /.gitconfig. This config file is for root user. You need to set git config for rstudio user because rstudio run on rstudio user. Below command is a temporary solution.
docker run -it -p 8787:8787 --env USERNAME="Carl" --env EMAIL=cboettig#example.com cboettig/ropensci-docker bash -c "cp /.gitconfig /home/rstudio; /usr/bin/supervisord"
It works!
Another solution is writing Dockerfile is based on cboettig/ropensci-docker. Below is sample Dockerfile.
FROM cboettig/ropensci-docker
RUN cp /.gitconfig /home/rstudio
CMD ["/usr/bin/supervisord"]
Related
Bottom line: output from container is not appearing in mounted local directory
I have read the documentation for bind mounts and on another project had success with this.
My docker file:
FROM ubuntu:18.04
RUN apt-get update && apt-get install -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev valgrind wget unzip git nano
# pulls ADBM from github and unzips in folder ADMBcode
RUN mkdir /ADMBcode
RUN wget https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-linux.zip
RUN mv admb-12.2-linux.zip /ADMBcode
RUN unzip ADMBcode/admb-12.2-linux.zip -d /ADMBcode
# pulls hydra repo from github into folder HYDRA
RUN mkdir /HYDRA
RUN git clone https://github.com/NOAA-EDAB/hydra_sim.git /HYDRA
# compiles and runs model
WORKDIR /HYDRA
RUN /ADMBcode/admb-12.2/admb hydra_sim.tpl
RUN ./hydra_sim
# create dir for output and move output
#RUN mkdir -p /HYDRA/output/diagnostics
#RUN mkdir /HYDRA/output/indices
# moves output to folder to be mounted
RUN mv *.out /HYDRA/output/diagnostics
RUN mv *.txt /HYDRA/output/indices
I build the image
podman build -t hydra .
and run the container using the following :
podman run --rm --name hydra --mount "type=bind,src=/path_on_local_machine/test,dst=/HYDRA/output" hydra
I have test folder on my local machine but the output is not mounted.
I have entered the container
podman run -it hydra
and checked that the output is there
I have done this before for another model and everything behaved. Not sure why this is not.
Any ideas what i am doing wrong?
Thanks
However
I have the following issue.
Failed to find a valid digest in the 'integrity' attribute for resource 'http://127.0.0.1:8080/uistatic/css/bootstrap4.0.0.min.css' with computed SHA-256 integrity 'xLbtJkVRnsLBKLrbKi53IAUvhEH/qUxPC87KAjEQBNo='. The resource has been blocked.
And this is happening when i put my site into docker with building this Dockerfile:
FROM python:3.6
COPY skfront /app
WORKDIR /app
RUN mkdir -p /static/resources
RUN mkdir logs
RUN mkdir certs
RUN pip3 install -r requirements.txt
RUN python3 manage.py collectstatic --settings blog_site.settings
EXPOSE 8080
CMD python3 website.py -l 0.0.0.0 -p 8080
This css is static file that doesn't change.
Any ideas why this is happening?
I found out that building Dockerfile on Windows can mess-up the final image.
When I build my site under Linux there ware no integrity errors.
I have a Dockerfile, it does dotnet publish and the dll's are copied to intermediate docker container. I would like to copy the dll's which are generated in container to my local system (Host) as well.
I believe we can use "cp" command to do that, but I am not able to find a solution to get the intermediate container Id to use the "cp" command.
syntax: docker cp CONTAINER:Container_Path Host_Path.
Please suggest me any other better solution for this scenario.
Dockerfile:
FROM microsoft/aspnetcore-build:1.1.4 as builder
COPY . /Code
RUN dotnet restore /Code/MyProj.csproj
RUN dotnet publish -c Release /Code/MyProj.csproj
RUN cp CONTAINER: /Code/bin/Release/netcoreapp1.1/publish /binaries
Thanks.
This answer is outside of the Dockerfile.
first your Dockerfile would have to have a volume.
[VOLUME] /my/path/in/container
To get files into and out of a volume, try using tar -cvf and tar -xvf to put and get files between a container and a host.
To put files from host's newfiles.tar in pwd to a container at /var/lib/neo4j/conf mount.
docker run --rm \
-v my-volume-data:/my/path/in/container -v $(pwd):/newfiles ubuntu bash -c \
"cd /my/path/in/container && tar -xf /newfiles/newfiles.tar"
To get files from into a container at /my/path/in/container mount to a host oldfiles.tar.
docker run --rm \
-v my-volume-data:/my/path/in/container -v $(pwd):/newfiles ubuntu bash -c \
"cd /my/path/in/container && tar -cf /newfiles/origfiles.tar"
The --user 1000:1000 is optional if your container has a user with uid of 1000.
It's unclear to me how to get my build files from the Gitlab CI (hosted on https://ci.gitlab.com) over to my personal server using rsync.
I have setup 1 test and 1 deploy job.
Under the deploy tab I have inputed the bash commands to:
Install rsync
Update packages
Finally, the rsync command to
transfer files over SSH to my personal server.
When I enter the SSH credentials (with verbose flag on) for my private personal server, it would appear that the SSH key is the issue. In Gitlab, I have already established the deploy key (for hooks - tested this and it works).
Where do I locate the public SSH key for the Gitlab deploy instance so that I can install that key on my server?
Below is the exact script entered in Gitlab CI deploy job script pane:
# Run as root
(
set -e
set -u
set -x
apt-get update -y
apt-get -y install rsync
)
git clone https://github.com/bla/deployments.git $HOME/deploy/deployments
SVR_WEB1_WEBSERVER="000.11.22.333"
USER1="franklin"
GROUP1="team1"
FROM_DIR="/gitlab-ci-runner/tmp/builds/myrepo-1/"
DEST1="subdomains/gitlab/myrepo"
EXCLUSIONS_LIST="${HOME}/deploy/deployments/exclusions/exclusions.txt"
ssh -v "$USER1#$SVR_WEB1_WEBSERVER"
/usr/bin/rsync -avzh --progress --delete -e ssh --group=$GROUP1 -p --exclude-from "$EXCLUSIONS_LIST" "$FROM_DIR" "$USER1#$SVR_WEB1_WEBSERVER:$DEST1"
Providing your private ssh key is dangerous unless you use your own gitlab-ci runners for deployment. That's why it is better to use rsync modules.
I am a bit new to docker and I have been trying to run deploy a meteor container with my meteor application. I have been using the dockerfile and instructions from https://registry.hub.docker.com/u/golden/meteor-dev/
However, I cant run docker run -p 3000:3000 -t -i -v /path/to/meteor/app:/opt/application -w /opt/application meteor-dev because my docker (version 0.5.3) does not recognize the flag (-w) to set the working directory.
Is there some workaround to set the working directory with docker 0.5.3? The work directory is already set in the docker file, but I guess I need to set it again when I run the container.
well, my workaround was to create a bash script that would go to the working directory and call the commands one by one. I created the bash script where my source is located "/path/to/meteor/app" and call docker run -p 3000:3000 -t -i -v /path/to/meteor/app:/opt/application meteor-dev bash /opt/application/start.sh with the bash as command and my script as argument