I have built and test a docker imagecustomop:latest. No there are certain files on my host system that I want to run using this docker image. So, for example, I have this file sample.py in my pwd and I want to run it using docker but without copying it on docker.
Is there any simple way to do it?
Related
I have a container that runs a Python script in order to download a few big files from Amazon S3. The purpose of this container is just to download the files so I have them on my host machine. Because these files are needed by my app (which is running in a separate container with a different image), I bind mount from my host to the app's container the directory downloaded from the first container.
Note 1: I don't want to run the script directly from my host as it has various dependencies that I don't want to install on my host machine.
Note 2: I don't want to download the files while the app's image is being built as it takes too much time to rebuild the image when needed. I want to pass these files from outside and update them when needed.
Is there a way to make the first container to download those files directly to my host machine without downloading them first in the container and then copying them to the host as they take 2x the space needed before cleaning up the container?
Currently, the process is the following:
Build the temporary container image and run it in order to download
the models
Copy the files from the container to the host
Cleanup unneeded container and image
Note: If there is a way to download the files from the first container directly to the second and override them if they exist, it may work too.
Thanks!
You would use a host volume for this. E.g.
docker run -v "$(pwd)/download:/data" your_image
Would run your_image and anything written to /data inside the container would actually write to the host in the ./download directory.
I am using Docker to containerize a Python script. If Docker wasn't in the picture, I would want pass a file path to the script, which would proceed to work on that file.
python coolscript.py data.csv
As a Docker novice, I'm not sure sure how to accomplish this. Currently, I am automatically executing the script when the container launches.
docker run coolcontainer python coolscript.py data.csv
Since the data.csv file path isn't known when the image is built, its not imported into the container and I cant seem to access it. I've seen some forums saying to mount the host filesystem, but that seems overkill since I just want one file. Is there a way to just send that one file into the container at runtime? How would you be architecting this?
The -v option for bind mounts then should do the trick:
docker container run -v /my/host/path:/my/container/path coolcontainer python /my/container/path/coolscript.py /my/container/path/data.csv
Place both files in /my/host/path
I am new to docker and containers. I have a container consisting of an MRI analysis software. Within this container are many other software the main software draws its commands from. I would like to run a single command from one of the softwares in this container using research data that is located on an external hard drive which is plugged into my local machine that is running docker.
I know there is a cp command for copying files (such as scripts) into containers and most other questions along these lines seem to recommend copying the files from your local machine into the container and then running the script (or whatever) from the container. In my case I need the container to access data from separate folders in a directory structure and copying over the entire directory is not feasible since it is quite large.
I honestly just want to know how I can run a single command inside the docker using inputs present on my local machine. I have run docker ps to get the CONTAINER_ID which is d8dbcf705ee7. Having looked into executing commands inside containers I tried the following command:
docker exec d8dbcf705ee7 /bin/bash -c "mcflirt -in /Volumes/DISS/FMRIPREP/sub-S06V1A/func/sub-S06V1A_task-compound_run-01_bold.nii -out sub-S06V1A_task-compound_run-01_bold_mcf_COMMAND_TEST.nii.gz -reffile /Volumes/DISS/FMRIPREP_TMP/sub-S06V1A_dof6_ver1.2.5/fmriprep_wf/single_subject_S06V1A_wf/func_preproc_task_compound_run_01_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots"
mcflirt is the command I want to run inside the container. I believe the exec command would do what I hope since if I run docker exec d8dbcf705ee7 /bin/bash -c "mcflirt" I will get help output for the mcflirt command which is the expected outcome in that case. The files inside of the /Volume/... paths are the files on my local machine I would like to access. I understand that the location of the files is the problem since I cannot tab complete the paths within this command; when I run this I get the following output:
Image Exception : #22 :: ERROR: Could not open image /Volumes/DISS/FMRIPREP/sub-S06V1A/func/sub-S06V1A_task-compound_run-01_bold
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Can anyone point me in the right direction?
So if I got you right, you need to execute some shell script and provide the context (like local files).
The way is straightforward.
Lets say your script and all needed files are located in /hello folder of your host PC (no matter really if they are stored together or not, just showing the technique).
/hello
- runme.sh
- datafile1
- datafile1
You mount this folder into your container to make the files accessible inside. If you dont need container to modify them, better mount in readonly mode.
You launch docker like this:
docker run -it -v /hello:/hello2:ro ubuntu /hello2/runme.sh
And that's it! Your script runme.sh gets executed inside container and it has access to nearby files. Thanks to -v /hello:/hello2:ro directive. It maps host's folder /hello into container's folder /hello2 in readonly ro mode.
Note you can have same names, I've just differed them to show the difference.
i am using native docker for mac and i have a small application running with docker container .
currently i am manually copying the data from my mac to docker container using docker cp command.
i want to make it dynamic, i want to put the data in my local directory which should get sync with docker container .
example:
mac local dir : users/vishnu/data/
which should get sync to
`<Docker-container-ID>:/opt/deploy/`
the container is already running ,i should not release the running container . i can only stop and start . is there a way ?? Thanks in advance
host mounted volume.
when you docker run you add a -v /Users/vishnu/data:/opt/deploy parameters.
if you need to add a mounted volume to your existing container, use the Kitematic UI. it's easier that way. but in general, you should add this when you docker run.
...
also, FYI - the idea that you can't delete a container is an anti-pattern with Docker. if you can't delete your container, because it would cause too many problems, you're doing something wrong. https://derickbailey.com/2017/04/05/what-i-learned-by-deleting-all-of-my-docker-images-and-containers/
How do I copy files from a docker container to the host machine during docker build command?
As a part of building my docker image for my app, I'm running some tests inside it, and I would like to copy the output of the test run into the host (which is a continuous integration server) to do some reporting.
I wouldn't run the tests during build, this will only increase the size of your image. I would recommend you to build the image and then run it mounting a host volume into the container and changing the working directory to the mount point.
docker run -v `pwd`/results:/results -w /results -t IMAGE test_script
There is no easy way to do this. Volumes are only created at run time. You can grab it out of the docker filesystem, (e.g. mine is /var/lib/docker/devicemapper/mnt/CONTAINER_ID/rootfs/PATH_TO_FILE) though there is no good way to figure out when your test process is complete. You could create a file when it's finished and do an inotify, but this is ugly.