docker: executable file not found in $PATH solution without changing CMD

Question

I am trying to run the official bwa docker https://hub.docker.com/r/biocontainers/bwa/, and I keep getting an error:

sudo docker run -u="root" -v ~/files/:/opt/inputs/ biocontainers/bwa "index /opt/inputs/hg19.fa"
docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index /opt/inputs/hg19.fa\": stat index /opt/inputs/hg19.fa: no such file or directory": unknown.
ERRO[0000] error waiting for container: context canceled

EDIT: Removing the double quotes from the lst string gives a different error:

sudo docker run -u="root" -v ~/files/:/opt/inputs/ biocontainers/bwa index /opt/inputs/hg19.fa
docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index\": executable file not found in $PATH": unknown.

I have found the reason behind it here:

docker: executable file not found in $PATH

This is the correct reason, but since this file was pre-build, and I want to use the official release, I cannot change the CMD synthax in Dockerfile. How can I make this work without changing the container itself?

BMitch · Accepted Answer · 2018-10-15 11:59:16Z

3

since this file was pre-build, and I want to use the official release, I cannot change the CMD synthax in Dockerfile

Actually you did change the setting of CMD in your run command. Everything after the image name overrides the default CMD value shipped with the image:

sudo docker run -u="root" -v ~/files/:/opt/inputs/ biocontainers/bwa "index /opt/inputs/hg19.fa"
docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index /opt/inputs/hg19.fa\": stat index /opt/inputs/hg19.fa: no such file or directory": unknown.
ERRO[0000] error waiting for container: context canceled

In this case, you have replaced the bwa value of CMD shipped in the Dockerfile with "index /opt/inputs/hg19.fa". Note the quotes and space are included in the executable you are trying to run. It is not trying to run index with an argument /opt/inputs/hg19.fa as you may have expected. This is why you see the error message:

"exec: \"index /opt/inputs/hg19.fa\": stat index /opt/inputs/hg19.fa: no such file or directory"

To run the command index, remove the quotes:

sudo docker run -u="root" -v ~/files/:/opt/inputs/ biocontainers/bwa index /opt/inputs/hg19.fa

answered Oct 15, 2018 at 11:59

BMitch

271k52 gold badges555 silver badges512 bronze badges

Sign up to request clarification or add additional context in comments.

6 Comments

Cindy Almighty Over a year ago

I am sorry, I posted the wrong error message, as I tried multiple versions of the command. I initially tried without it, and the error is: docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index\": executable file not found in $PATH": unknown.

BMitch Over a year ago

If you need a binary that is not included with the image you've selected, you'll need to pick a different image, extend image, or include the install of that binary with your running of the image.

Cindy Almighty Over a year ago

Got it, just add bwa. Accepted the answer. Can you tell me how to not override the command but add arguments to it? Is that even possible if the last line is: CMD ["bwa"] ?

BMitch Over a year ago

The value is CMD is always overridden, not extended. It sounds like you're looking for the behavior of ENTRYPOINT. docs.docker.com/engine/reference/builder/…

Cindy Almighty Over a year ago

Then why specify such a CMD? Which cannot possibly do anything, apart from print help.

|

Collectives™ on Stack Overflow

docker: executable file not found in $PATH solution without changing CMD

1 Answer 1

6 Comments

Your Answer

Linked

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

6 Comments

Your Answer

Sign up or log in

Post as a guest

Linked

Related