trying to bash into container and do a for loop which simply performs a command (which works on a single file by the way). it even seems to echo the right command...what did I forget
Untitled
for pdf in *.pdf ;
do
docker run --rm -v "$(pwd):/home/docker" leofcardoso/pdf2pdfocr -g jpeg2000 -v -i '\'''$pdf''\''';
done
You can bash in a container with this commands:
To see the docker container id
docker container ls
To enter in bash inside a container.
docker exec -it CONTAINER_ID bash
First thing, you are not allocating tty in the docker run command and the docker container dies soon after converting files. Here is main process of container
#!/bin/bash
cd /home/docker
exec pdf2pdfocr.py "$#"
So, in this case, the life of this container is the life of exec pdf2pdfocr.py "$#" command.
As mentioned by #Fra, override the entrypoint and run the command manually.
docker run --rm -v "$(pwd):/home/docker" -it --entrypoint /bin/bash leofcardoso/pdf2pdfocr
but in the above run command, docker container will do not a thing and will just allocate the tty and the bash will open. So you can convert files inside your containers using docker exec and then run pdf2pdfocr.py -g jpeg2000 -v -i mypdf.pdf
So, if you want to run with override entry point then you can try.
docker run -it --rm --entrypoint /bin/bash -v "$(pwd):/home/docker" leofcardoso/pdf2pdfocr -c "pdf2pdfocr.py -g jpeg2000 -v -i mypdf.pdf"
or with the bash script
#!/bin/bash
for pdf in *.pdf ;
do
echo "converting $pdf"
docker run -it --rm --entrypoint /bin/bash -v "$(pwd):/home/docker" leofcardoso/pdf2pdfocr -c "pdf2pdfocr.py -g jpeg2000 -v -i $pdf"
done
But the container will die after completing the conversion.
Related
I am using a tool (gatk) distributed as a docker image and try to use its commands in a shell script.
I run the docker in detached mode.
sudo docker run --name my_container -d -v ~/test:/gatk/data -it broadinstitute/gatk:4.1.9.0
Then I run the commands from shell script
#!/bin/bash
docker exec my_container gatk command1
wait
docker exec my_container gatk command2
command2 needs input from command1 so I use wait, but still command2 is executed before command 1 is finished.
I also tried
#!/bin/bash
docker exec my_container gatk command1
docker wait my_container
docker exec my_container gatk command2
but then the script does not continue running after command1 is completed.
I managed to solve it. The problem was is that when I ran docker exec I did not define it to receive input from the shell. Adding -i flag to docker exec solved the problem. Here is the full solution.
I start docker in detached mode
sudo docker run --name my_container -d -v ~/test:/gatk/data -it broadinstitute/gatk:4.1.9.0
Now I can close the terminal, the docker container is up and running and I can use it in a new terminal.
I generate a bash script called myscript.sh with the following code.
#!/bin/bash
docker exec -i my_container gatk command1
wait
docker exec -i my_container gatk command2
I run the script, disown it and close the terminal.
./myscript.sh&disown;exit
You can run both commands in a single shot:
docker run image /bin/bash -c "gatk command1 && gatk command2"
To run a bash terminal in a Docker container I can run the following:
$ docker exec -it <container> /bin/bash
However, I want to execute a command in the container automatically. For example, if I want to open a bash terminal in the container and create a file I would expect to run something like:
docker exec -it <container> /bin/bash -c "touch foo.txt"
However, this doesn't work... Is there a simple way to achieve this? Of course, I could type the command after opening the container, but I want to open a bash terminal and run a command at the same time.
You can run your touch command and then spawn another shell :
docker exec -it <container> /bin/bash -c "touch foo.txt; exec bash"
Works perfectly fine for me
~# docker run -tid --rm --name test ubuntu:20.04
~# docker exec -it test /bin/bash -c "touch /foo.txt"
~# docker exec -it test /bin/bash
root#b6b0efbb13be:/# ls -ltr foo.txt
-rw-r--r-- 1 root root 0 Mar 7 05:35 foo.txt
Easy solution:
docker exec -it <container> touch foo.txt
You can verify
docker exec -it <container> ls
This was tested with alpine image.
Remember that in docker images there is a entrypoint and a command. Now we are editing the command of the default entrypoint for alpine, via docker exec
It depends of the entrypoint if env variablers are load or not, $PATH ..., so other images maybe you need to write /bin/touch or /usr/bin/ls
Good luck!
When you run docker exec -it <container> /bin/bash -c "touch foo.txt", container sends 0 exit code so that it means the task is done and you'll be returned to your host.
When you run docker exec -it <container /bin/bash, bash shell is not terminated until you explicitly type exit or use CTRL+D in bash environment. bash is continuously running.
This is why when you run the second command, it goes to bash, runs your command (touches) and then exits.
I'd like to know if there's a way to do this
Let's say the dockerfile contains this line, that specifies path of an executable
ENV CLI /usr/local/bin/myprogram
I'd like to be able to call this program using ENV variable name through exec command.
For example
docker exec -it <my container> 'echo something-${CLI}
Expecting
something-/usr/local/bin/myprogram
However that returns:
OCI runtime exec failed: exec failed: container_linux.go:348: starting container process caused "exec: \"${CLI} do something\": executable file not found in $PATH": unknown
Ok, I found a way to do it, all you need to do is evaluate command with bash
docker exec -it <container id> bash -c 'echo something-${CLI}'
returns something-/usr/local/bin/myprogram
If the CLI environment variable is not already set in the container, you can also pass it in such as:
docker exec -it -e CLI=/usr/local/bin/myprogram <container id> bash -c 'echo something-${CLI}'
See the help file:
docker exec --help
Usage: docker exec [OPTIONS] CONTAINER COMMAND [ARG...]
Run a command in a running container
Options:
-d, --detach Detached mode: run command in the background
-e, --env list Set environment variables
....
In it's original revision docker exec -it <my container> '${CLI} do something' with the expectation that ${CLI} will be substituted with /usr/local/bin/myprogram (as the exec COMMAND) and everything after passed as ARG's to /usr/local/bin/myprogram will not work, this is clearly documented: https://docs.docker.com/engine/reference/commandline/exec/
COMMAND should be an executable, a chained or a quoted command will not work. Example:
docker exec -ti my_container "echo a && echo b" will not work, but
docker exec -ti my_container sh -c "echo a && echo b" will.
Following the documentation, this will work as expected: docker exec -ti my_container sh -c "${CLI} foo", ${CLI} will be be executed after variable expansion and the argument(s) passed to the shell script set in ${CLI} (e.g. sh -c /usr/local/bin/myprogram foo).
Alternatively you could set the ENTRYPOINT to your script and pass in arguments with CMD or at the command line with docker run for example:
Given the below directory structure:
.
├── Dockerfile
└── example.sh
The Dockerfile contents:
FROM ubuntu:18.04
COPY example.sh /bin
RUN chmod u+x /bin/example.sh
ENTRYPOINT ["/bin/example.sh"]
CMD ["bla"]
And the example.sh script contents:
#!/bin/bash
echo $1
The CMD specified in the Dockerfile after the ENTRYPOINT will be the default argument for your script and you can override the default argument on the command line (assuming that the image is built and tagged as example:0.1):
user#host> docker run --rm example:0.1
bla
user#host> docker run --rm example:0.1 "arbitrary text"
arbitrary text
Note: this is my go to article for differences between ENTRYPOINT and CMD in Dockerfile's: https://medium.freecodecamp.org/docker-entrypoint-cmd-dockerfile-best-practices-abc591c30e21
I'm attempting to craft system admin bash tools for starting up a Docker image.
But such docker run keeps dying on me after its bash script exited.
The actual working bash script in question is:
#!/bin/sh
docker run \
--name publicnginx1 \
-v /var/www:/usr/share/nginx/html:ro \
-v /var/nginx/conf:/etc/nginx:ro \
--rm \
-p 80 \
-p 443 \
-d \
nginx
docker ps
Executing the simple script resulted in:
# ./docker-run-nginx.sh
743a6eaa33f435e3e0d211c4047bc9af4d4667dc31cd249e481850f40f848c83
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
743a6eaa33f4 nginx "nginx -g 'daemon of…" 1 second ago Up Less than a second 0.0.0.0:32778->80/tcp, 0.0.0.0:32777->443/tcp publicnginx1
And after that bash script gets completed, I executed 'docker ps'
# docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
There is no Docker running.
What did I do wrong?
Try to run it without --rm.
You can see all container (including the one that already died using this command):
> docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS
743a6eaa33f4 nginx "nginx -g 'daemon of…" 1 second ago Exited (??) ??
^^^^^
You should be able to look at what is the exit code of the container. Using the container id, you can also look into it's log to understand better what is going on:
docker logs 743a6eaa33f4
If you still can't figure it out, you can start the container with tty to run bash, and try to run the command inside it.
docker run -it -v /var/www:/usr/share/nginx/html:ro -v /var/nginx/conf:/etc/nginx:ro --rm -p 80 -p 443 nginx bash
Is there any shortcut command to connect to a docker container without running docker exec -it 'container_id' bash every time?
Here is a shorter command line shortcut to:
Check if a container is running
If running, connect to a running container using docker exec -it <container> bash command:
Script docker-enter:
#!/bin/bash
name="${1?needs one argument}"
containerId=$(docker ps | awk -v app="$name:" '$2 ~ app{print $1}')
if [[ -n "$containerId" ]]; then
docker exec -it $containerId bash
else
echo "No docker container with name: $name is running"
fi
Then run it as:
docker-enter webapp
I'm using the following alias on OS X:
alias dex='function _dex(){ docker exec -i -t "$(basename $(pwd) | tr -d "[\-_]")_$1_1" /bin/bash -c "export TERM=xterm; exec bash" };_dex'
In the same directory as my docker-files, I run "dex php" to enter the PHP container.
If random id is complicated. Start container with name docker run --name test image and connect with its name docker exec -it test bash.