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Question: How to label a dataset as a particular datatype in a shared library
1
gravatar for alex
19 months ago by
alex • 40
alex • 40 wrote:

I'm a galaxy admin, and I'm running my galaxy on a server with a bunch of genomes in a folder called /globus. Under the admin panel, I've added the entire directory structure under /globus/a_group_of_patients as a shared data library.

However, I can't set the type of the bam files as "bam" in the shared data library UI -- it says "feature coming soon". When I saw that, I decided to spend the couple hours needed to update from 16.01 to 17.01, but I was surprised to find that in 17.01 the feature is still "coming soon".

  1. Is there another way to set the datatype than in the shared library UI?

  2. When I initally did the import, I set the data-type as "auto-detect". Why didn't it auto-detect "bam" on all the files with extension ".bam" or "fastq" on all the files with a ".fastq" extension?

  3. Is this feature still "coming soon" (e.g. in 17.05) or has it fallen off the roadmap?

Thanks,

data library shared data • 520 views
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modified 19 months ago by Martin Čech ♦♦ 4.9k • written 19 months ago by alex • 40
0
gravatar for Martin Čech
19 months ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

I am sorry about this alex - entirely my fault.

  1. You can try using the old library UI that is under the Admin menu. It will only allow you to change one dataset at a time though.
  2. Auto detection should work. Did you check Galaxy logs for errors? Do you have samtools on path? (I think it is used to detect bam files)
  3. I have actually started to work on adding this feature this month but it will not make it to the 17.05 due to prioritization.

Alternatively can you set the datatype to 'bam' during the import to library?

Sorry again,

Martin
ADD COMMENT • link written 19 months ago by Martin Čech ♦♦ 4.9k
1

No worries Martin, I understand things sometimes fall by the wayside! Adding them one by one in the admin UI isn't too terrible.

ADD REPLY • link written 19 months ago by alex • 40
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