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UMMS-Biocore / dolphinnext

A graphical user interface for distributed data processing of high throughput genomics
https://dolphinnext.umassmed.edu
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Tutorial issues #287

Open tomgreen66 opened 4 years ago

tomgreen66 commented 4 years ago

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:

  1. Follow instructions at https://github.com/UMMS-Biocore/dolphinnext-tutorial
  2. Get to https://github.com/UMMS-Biocore/dolphinnext-tutorial#creating-collection
  3. Add /data/fastq_data/single and click search
  4. See error

Expected behavior List of files to add to collection.

Screenshots image

Desktop (please complete the following information):

Additional context Add any other context about the problem here.

tomgreen66 commented 4 years ago

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.

nephantes commented 4 years ago

Thanks Tom! We'll check an fix the problem

tomgreen66 commented 4 years ago

Thanks. Also got a couple of other questions with tutorial - new issues?

  1. --privileged in the docker command - is that really required?
  2. 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 the user_add.sh in the docker container will fix this.
nephantes commented 4 years ago
  1. 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.
  2. We will add the extra instructions.