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Tutorial issues
Describe the bug Using the instructions at https://github.com/UMMS-Biocore/dolphinnext-tutorial I find myself hitting an issue at the https://github.com/UMMS-Biocore/dolphinnext-tutorial#creating-collection
I cant seem to add the files from /data/fastq_data/single
and get the following:
Query failed! Please check your query, connection profile, or internet connection.
To Reproduce Steps to reproduce the behavior:
- Follow instructions at https://github.com/UMMS-Biocore/dolphinnext-tutorial
- Get to https://github.com/UMMS-Biocore/dolphinnext-tutorial#creating-collection
- Add
/data/fastq_data/single
and click search - See error
Expected behavior List of files to add to collection.
Screenshots
Desktop (please complete the following information):
- OS: Windows 10
- Browser Firefox
- Version 78.0.2
Additional context Add any other context about the problem here.
Having just tried again just to make sure it seems to work. As you can see from screenshot above I definitely got the error message. Very strange - maybe since I quit from container and loaded again it did something. Maybe report will still help.
Thanks Tom! We'll check an fix the problem
Thanks. Also got a couple of other questions with tutorial - new issues?
-
--privileged
in the docker command - is that really required? - When I run the test job it uses the
docker
user to ssh to localhost and create a directory in/export/tests
but docker cannot create it since it doesnt have the rights and job fails. Making a directory/export/tests
with docker ownership fixes it. Maybe extra instruction at beginning of tutorial or in theuser_add.sh
in the docker container will fix this.
- In our tutorial we are doing a test run in docker. To be able to run singularity in a docker container, you need to run docker with --privileged. If you are not going to run it inside of docker, you don't need that.
- We will add the extra instructions.