I have a script on the docker host that i want to run and create symbolic links inside its containers. However, i cannot seem to get the symbolic link created when i run my script below:
#!/bin/bash
declare -A containers
while IFS== read -r key value; do
containers[$key]=${value}
S=$(sudo docker exec -t $key ln -s /srv/my.cnf /etc/mysql/my.cnf);
done < "/opt/containers.txt"
The weird thing is that when i run the command outside the script directly in the terminal, it actually works. E.g.,
sudo docker exec -t db-test-1 ln -s /srv/my.cnf /etc/mysql/my.cnf
So not sure why it won't run in the script. Any suggestions?
For testing, you can see if isolating the command (here ln) in its own shel helps:
S=$(sudo docker exec -t $key /bin/sh -c "ln -s /srv/my.cnf /etc/mysql/my.cnf");
Related
I have a simple bash script 'test.sh' in the root of mounted folder :
#!/bin/bash
Rscript -e "source('/home/rstudio/mount-folder/src/controller.R')";
However, when i try to mount folder and start the container with docker run as follows:
docker run -d -p 8000:8787 -e ROOT=true -e DISABLE_AUTH=true --name container -v mount-folder/:/home/rstudio/ image_name /home/rstudio/test.sh
above run command starts the container but exits automatically.
I am looking for a docker run command that starts the container , mounts the folder and then executes the bash script which is in the mount-folder without exiting the container.
(** dont want to go with docker exec command as it is not suitable for my use case for other reasons)
Dockerfile:
FROM rocker/rstudio:4.0.2
//some RUN commands to install necessary r packages
EXPOSE 8787
CMD tail -f /dev/null
Other details :
Image that i am using is rstudio server from rocker and container runs on AWS ubuntu machine.
Edit :
have also tried adding CMD tail -f /dev/null at the end of dockerfile as suggested in http://bigdatums.net/2017/11/07/how-to-keep-docker-containers-running/ even then the container exits.
Docker containers shutdown automatically when run in detached mode. I think this article proposes a nice solution:
http://bigdatums.net/2017/11/07/how-to-keep-docker-containers-running/
You could add tail -f /dev/null as the last command in your bash script instead so that the script will never halt unless it is told to do so.
When you do docker run [options] image_name [cmd] the command you specify becomes the command for the container and replaces any the command specified in the dockerfile (that's why adding CMD tail -f /dev/null doesn't do anything). If you ran your container without the /home/rstudio/test.sh at the end, it should stay running.
The solution would be to update your script to add the tail command at the end.
#!/bin/bash
Rscript -e "source('/home/rstudio/mount-folder/src/controller.R')";
exec tail -f /dev/null
If you can't update that script, you could instead add it to the command being passed to the container, with something like:
docker run [options] image_name bash -c '/home/rstudio/test.sh && exec tail -f /dev/null'
I'm trying to create an alias to help debug my docker containers.
I discovered bash accepts a --init-file option which ought to let us run some commands before passing over to interactive mode.
So I thought I could do
docker-bash() {
docker run --rm -it "$1" bash --init-file <(echo "ls; pwd")
}
But those commands don't appear to be running:
% docker-bash c7460dfcab50
root#9c6f64a9db8c:/#
Is it an escaping issue or.. what's going on?
bash --init-file <(echo "ls; pwd")
Alone in a terminal on my host machine works as expected (runs the command starts a new bash instance).
In points:
The <(...) is a bash extension process subtitution.
From the manual above: Process substitution is supported on systems that support named pipes (FIFOs) or the /dev/fd method of naming open files..
The process substitution works like this:
bash creates a fifo in /tmp or creates a new file descriptor in /dev/fd.
The filename, either the /tmp/.something or /dev/fd/<number> is substituted for <(...) when command is executed.
So for example echo <(echo 1) outputs /dev/fd/63.
Docker works by creating a new environment that is separated from the host. That means that:
Processes inside docker do not inherit file descriptors from the host process:
So /dev/fd/* files are not inherited.
Processes inside docker are accessing isolated filesystem tree.
So processes can't access /tmp/* files from the host.
So summarizing docker run -ti --rm alpine cat <(echo 1) will not work, because the filename substituted by <(...) is not available from docker environment.
An easy workaround would be to just:
docker run -ti --rm alpine sh -c 'ls; pwd; exec sh'
Or use a temporary file:
echo "ls; pwd" > /tmp/tempfile
docker run -v /tmp/tempfile:/tmp/tempfile bash bash --init-file /tmp/tempfile
For my use-case I wanted to set an alias which won't persist if we re-exec the shell. However, aliases can be written to ~/.bashrc which will be reloaded on the subsequent exec. Ergo,
docker-bash() {
docker run --rm -it "$1" bash -c $'set -o xtrace; echo "alias ll=\'ls -lAhtrF --color=always\'" >> ~/.bashrc; exec "$0"'
}
Works. --rm should clean up any files we create anyway if I understand properly how docker works.
Or perhaps this is a nicer way to write it:
docker-bash() {
read -r -d '' BASHRC << EOM
alias ll='ls -lAhtrF --color=always'
EOM
docker run --rm -it "$1" bash -c "echo \"$BASHRC\" >> ~/.bashrc; exec \"\$0\""
}
I want to open a interactive shell which sources a script to use the bitbake environment on a repository that I bind mount:
docker run --rm -it \
--mount type=bind,source=$(MY_PATH),destination=/mnt/bb_repoistory \
my_image /bin/bash -c "cd /mnt/bb_repoistory/oe-core && source build/conf/set_bb_env.sh"
The problem is that the -it argument does not seem to have any effect, since the shell exits right after executing cd /mnt/bb_repoistory/oe-core && source build/conf/set_bb_env.sh
I also tried this:
docker run --rm -it \
--mount type=bind,source=$(MY_PATH),destination=/mnt/bb_repoistory \
my_image /bin/bash -c "cd /mnt/bb_repoistory/oe-core && source build/conf/set_bb_env.sh && bash"
Which spawns an interactive shell, but none of the macros defined in set_bb_env.sh
Would there be a way to provide a tty with the script properly sourcered ?
The -it flag is conflicting with the command to run in that you're telling docker to create the pseudo-terminal (ptty), and then running a command in that terminal (bash -c ...). When that command finishes, then the run is done.
What some people have done to work around this is to only have export variables in their sourced environment, and the last command would be exec bash. But if you need aliases or other items that aren't inherited like that, then your options are a bit more limited.
Instead of running the source in a parent shell, you could run it in the target shell. If you modified your .bash_profile to include the following line:
[ -n "$DOCKER_LOAD_EXTRA" -a -r "$DOCKER_LOAD_EXTRA" ] && source "$DOCKER_LOAD_EXTRA”
and then had your command be:
... /bin/bash -c "cd /mnt/bb_repository/oe-core && DOCKER_LOAD_EXTRA=build/conf/set_bb_env.sh exec bash"
that may work. This tells your .bash_profile to load this file when the env variable is already set, but not otherwise. (There can also be the -e flag on the docker command line, but I think that sets it globally for the entire container, which is probably not what you want.)
I'm trying to run MULTIPLE commands like this.
docker run image cd /path/to/somewhere && python a.py
But this gives me "No such file or directory" error because it is interpreted as...
"docker run image cd /path/to/somewhere" && "python a.py"
It seems that some ESCAPE characters like "" or () are needed.
So I also tried
docker run image "cd /path/to/somewhere && python a.py"
docker run image (cd /path/to/somewhere && python a.py)
but these didn't work.
I have searched for Docker Run Reference but have not find any hints about ESCAPE characters.
To run multiple commands in docker, use /bin/bash -c and semicolon ;
docker run image_name /bin/bash -c "cd /path/to/somewhere; python a.py"
In case we need command2 (python) will be executed if and only if command1 (cd) returned zero (no error) exit status, use && instead of ;
docker run image_name /bin/bash -c "cd /path/to/somewhere && python a.py"
You can do this a couple of ways:
Use the -w option to change the working directory:
-w, --workdir="" Working directory inside the container
https://docs.docker.com/engine/reference/commandline/run/#set-working-directory--w
Pass the entire argument to /bin/bash:
docker run image /bin/bash -c "cd /path/to/somewhere; python a.py"
You can also pipe commands inside Docker container, bash -c "<command1> | <command2>" for example:
docker run img /bin/bash -c "ls -1 | wc -l"
But, without invoking the shell in the remote the output will be redirected to the local terminal.
bash -c works well if the commands you are running are relatively simple. However, if you're trying to run a long series of commands full of control characters, it can get complex.
I successfully got around this by piping my commands into the process from the outside, i.e.
cat script.sh | docker run -i <image> /bin/bash
Just to make a proper answer from the #Eddy Hernandez's comment and which is very correct since Alpine comes with ash not bash.
The question now referes to Starting a shell in the Docker Alpine container which implies using sh or ash or /bin/sh or /bin/ash/.
Based on the OP's question:
docker run image sh -c "cd /path/to/somewhere && python a.py"
If you want to store the result in one file outside the container, in your local machine, you can do something like this.
RES_FILE=$(readlink -f /tmp/result.txt)
docker run --rm -v ${RES_FILE}:/result.txt img bash -c "grep root /etc/passwd > /result.txt"
The result of your commands will be available in /tmp/result.txt in your local machine.
For anyone else who came here looking to do the same with docker-compose you just need to prepend bash -c and enclose multiple commands in quotes, joined together with &&.
So in the OPs example docker-compose run image bash -c "cd /path/to/somewhere && python a.py"
If you don't mind the commands running in a subshell, just put a set of outer parentheses around the multiple commands to run:
docker run image (cd /path/to/somewhere && python a.py)
TL;DR;
$ docker run --entrypoint /bin/sh image_name -c "command1 && command2 && command3"
A concern regarding the accepted answer is below.
Nobody has mentioned that docker run image_name /bin/bash -c just appends a command to the entrypoint. Some popular images are smart enough to process this correctly, but some are not.
Imagine the following Dockerfile:
FROM alpine
ENTRYPOINT ["echo"]
If you try building it as echo and running:
$ docker run echo /bin/sh -c date
You will get your command appended to the entrypoint, so that result would be echo "/bin/sh -c date".
Instead, you need to override the entrypoint:
$ docker run --entrypoint /bin/sh echo -c date
Docker run reference
In case it's not obvious, if a.py always needs to run in a particular directory, create a simple wrapper script which does the cd and then runs the script.
In your Dockerfile, replace
CMD [ 'python', 'a.py' ]
or whatever with
CMD [ '/wrapper' ]
and create a script wrapper in your root directory (or wherever it's convenient for you) with contents like
#!/bin/sh
set -e
cd /path/to/somewhere
python a.py
In many situations, perhaps also consider rewriting a.py so that it doesn't need a wrapper. Either make it os.chdir() where it needs to be, or have it look for its data files in a directory you configure in its environment or similar.
So i've written a Dockerfile for a project, i've defined a CMD to run on starting the container to bootstrap the application.
The Dockerfile looks like
# create our mount folders and volumes
ENV MOUNTED_VOLUME_DIR=sites
RUN mkdir /$MOUNTED_VOLUME_DIR
ENV PATH=$MOUNTED_VOLUME_DIR/sbin:$MOUNTED_VOLUME_DIR/common/bin:$PATH
RUN chown -Rf www-data:www-data /$MOUNTED_VOLUME_DIR
# Mount folders
VOLUME ["/$MOUNTED_VOLUME_DIR/"]
# Expose Ports
EXPOSE 443
# add our environment variables to the server
ADD ./env /env
# Add entry point script
ADD ./start.sh /usr/bin/startContainer
RUN chmod 755 /usr/bin/startContainer
# define entrypoint command
CMD ["/bin/bash", "/usr/bin/startContainer"]
The start.sh script, does some git stuff like cloning the right repo, setting environment vars, as well as starting supervisor.
The start script begins with this
#!/bin/bash
now=$(date +"%T")
echo "Container Start Time : $now" >> /tmp/start.txt
/usr/bin/supervisord -n -c /etc/supervisord.conf
I start my new container like this
docker run -d -p expoPort:contPort -t -i -v /$MOUNTED_VOLUME_DIR/$PROJECT:/$MOUNTED_VOLUME_DIR $CONTAINER_ID /bin/bash
when i login to the container i see that supervisor hasn't been started, and neither has nginx or php5-fpm. the /tmp/start.txt file with a timestamp set from the startContainer script doesn't exist, showing its never ran the CMD in the Dockerfile.
Any hints on to get this fixed would be great
This:
docker run -d -p expoPort:contPort -t -i -v /$MOUNTED_VOLUME_DIR/$PROJECT:/$MOUNTED_VOLUME_DIR $CONTAINER_ID /bin/bash
Says 'run /bin/bash' after instantiating the container. E.g. skip CMD.
Try this:
docker run -d -p expoPort:contPort -t -i -v /$MOUNTED_VOLUME_DIR/$PROJECT:/$MOUNTED_VOLUME_DIR $CONTAINER_ID