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ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
MIT License
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Docker image issue? #224

Closed tbrunetti closed 4 years ago

tbrunetti commented 4 years ago

Hello,

This issue is likely due to user error -- sorry I am relatively new to Docker. I am trying to build your docker image by running the following from your github site and then using Cromwell to manage the workflow but I am having trouble with generating a docker image:

sudo docker build atac-seq-pipeline/dev/docker_image/

There seems to be a lot of conflicting python version and python library issues. If I try to update them in the DockerFile, it will resolve one problem but have an issue with a different python library that conflicts with a python version issue with what I updated. The main culprits seem to be metaseq, pybedtools, and scikit-learn.

Here is the stdout/err file: stdout.txt

Any suggestions or help would be very much appreciated!

tbrunetti commented 4 years ago

I ended up using a pre-made image instead and it seems to work but now when I run the following command:

sudo java -jar -Dconfig.file=backend.conf cromwell-42.jar run test_filter.wdl -i test_filter.json -o workflow_opts/docker.json

I get the following error when using the test data. Any suggestions? stdout_new.txt

leepc12 commented 4 years ago

You don't need to build it. Just pull it from repo.

docker pull quay.io/encode-dcc/atac-seq-pipeline:v1.7.0

That command line is for our integration test (not for users). There are several configuration (fetching test data from Google Cloud Storage, downloading cromwell, ...) needed before running that command line.

See ./test.sh on that directory for details.