Docker failing to find executable files within blobtoolkit:latest

[BirdmanRidesAgain]

Hi,

I'm trying to run blobtoolkit from the docker file, and I'm running into some issues while following the README to get the package up and running.

I ran the pull command (docker pull genomehubs/blobtoolkit) from your docker repository (https://hub.docker.com/r/genomehubs/blobtoolkit), and it seemed to install alright.

The first thing I did was attempt to use the interactive viewer (code below). After specifying the platform (amd64 vs. my default arm64), that had the desired behavior - a container named btk is created and the viewer loads at 'http://localhost:8080/view/all'.

docker run -d --rm --name btk --platform linux/amd64 \ -v /Users/keilercollier/Documents/tools/blobtoolkit/datasets \ -v /Users/keilercollier/Documents/tools/blobtoolkit/output \ -p 8000:8000 -p 8080:8080 \ -e VIEWER=true \ genomehubs/blobtoolkit:latest

I then attempted to run the provided code to create a minimal dataset from a local assembly. (A giant clam, in this case.)

docker run -it --rm --name btk -u 1000 \ --platform linux/amd64 \ -v /Users/keilercollier/Documents/tools/blobtoolkit/datasets \ -v /Users/keilercollier/Documents/tools/blobtoolkit/databases \ -v /Users/keilercollier/Documents/tools/blobtoolkit/data \ -v /Users/keilercollier/Documents/tools/blobtoolkit/output \ genomehubs/blobtoolkit:latest \ ./blobtools2/blobtools create \ --fasta data/Tridacna_squamosina_flye_racon.fasta \ --taxid 484284 \ --taxdump taxdump \ datasets/giant_clam

This is the output: docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "./blobtools2/blobtools": stat ./blobtools2/blobtools: no such file or directory: unknown.

It doesn't seem to be able to find the directories and I'm not sure how to fix that. Running it without the -u argument (or with my local/root user ID) produces the same output, as does running any other command which needs './blobtools2/blobtools' as an argument (eg, 'blobtools add'). Removing the platform argument produces the same error, and adds the previously-solved one about system incompatibility.

Hoping you might have some insight on this, and thanks in advance for your time!

[rjchallis]

Hi

To run the commands inside the container, there is no need for the ./blobtools2/ prefix as the blob tools command is in the PATH. So your command should work if you run it as

blobtools create \
 --fasta data/Tridacna_squamosina_flye_racon.fasta \
 --taxid 484284 \
 --taxdump taxdump \
 datasets/giant_clam

[BirdmanRidesAgain]

Works perfectly! Thanks- I'm not used to using docker yet, and I wasn't sure how to see the directory structure in there. Makes a bit more sense now.

[github-actions[bot]]

This issue has being marked as dormant because blobtoolkit-docker is being archived. The code is now part of the main BlobToolKit repository.

If you feel the issue has not been resolved, please follow the updated BlobToolKit installation instructions to first confirm that you are using the latest version, and then open a new issue at the main BlobToolKit repository if necessary.

This issue will be automatically closed in 7 days.

[github-actions[bot]]

This issue was closed because it has been inactive for 7 days since being marked as dormant.