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Published 20 hours ago • verified publisher icon higlass

Delete/organize list entries from HiGlass.io

Open gibcus opened this issue 6 years ago • 7 comments

According to the HiGlass.io documentation, there is an option to use the –project-name parameter with the ingest command. This would allow collapsing by grouping tilesets together as projects.

I got it to work and it's a great step forward!

Yet, there ENORMOUS amount of libraries pulled from HiGlass.io that are unorganized and they clutter up my (large) list of libraries. I can delete my own entries with list_tilesets / delete_tileset

Is there any way to organize/delete the pulled libraries?

gibcus avatar May 23 '19 20:05 gibcus

You should be able to use the --no-public-data option to hide all of the libraries that come from higlass.io. Let me know if that doesn't work and I can investigate.

pkerpedjiev avatar May 23 '19 21:05 pkerpedjiev

I was hoping for something like that and I'd love to apply it! I just can't find where to apply the option. Is it an option to higlass-server/manage.py?

gibcus avatar May 24 '19 01:05 gibcus

It's an option for higlass-manage. You should be able to do higlass-manage start --no-public-data.

pkerpedjiev avatar May 24 '19 21:05 pkerpedjiev

We installed higlass-manage on our server and I seem to be able to start higlass on my preferred port. Unfortunately, I still get public data when using --no-public-data. Would it work with a modified .json using --default-track-options?

gibcus avatar May 25 '19 19:05 gibcus

Must be a bug. This is a high priority issue so I'll try to investigate this week. Thanks for trying and reporting.

pkerpedjiev avatar May 27 '19 03:05 pkerpedjiev

Also, would you mind pasting in the exact command you're using to start it? I just tried it at home using higlass-manage start --no-public-data and don't see any of the datasets from higlass.io.

Can you make sure you're using the latest version: v0.7.1? You can run higlass-manage version to find out. If it says that that command can't be found, then you're running an older version. You can also do pip freeze | grep higlass-manage.

pkerpedjiev avatar May 27 '19 04:05 pkerpedjiev 

higlass-manage start \
--no-public-data \
--temp-dir /data/users/gibcus/chicken2.0/hg-tmp/ \
--data-dir /data/users/gibcus/chicken2.0/hg-data/ \
-p 8765 \
-s http://old-dell.ad.umassmed.edu \
-n chicken2.0

We're running higlass-manage==0.7.0 I'll ask @sergpolly to update to v0.7.1 on the server

gibcus avatar May 27 '19 13:05 gibcus