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higlass / higlass-docker

Builds a docker container wrapping higlass-server and higlass-client in nginx
MIT License
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Change list of pre-installed tracks/datasets #144

Open danledinh opened 6 years ago

danledinh commented 6 years ago

Hi, is there a way to remove some pre-installed tracks/datasets?

I'm currently using the Django admin page to manage my own data, but I'd like to make some changes to the default list.

Thanks!

pkerpedjiev commented 6 years ago

Yup. In the django admin interface, under the viewconfs table you should find an entry for 'default'. In that viewconf, you'll find a list called trackSourceServers. If you take out higlass.io it should remove all the foreign datasets from the list.

danledinh commented 6 years ago

Cool. Is there a way to select a subset of the data? I.e. I'd like to keep the hg38 chromosome annotations.

pkerpedjiev commented 6 years ago

Unfortunately right now there isn't. Sorry about that.

danledinh commented 6 years ago

ok. Thanks!

danledinh commented 6 years ago

I was able to create and ingest gene annotation files. What kind of file is necessary to correctly display the position search box?

The screenshot shows my position search box but the coordinates are fixed: image

pkerpedjiev commented 6 years ago

You need to upload a chromSizes file and set it coordSystem parameter.

docker exec higlass-container python higlass-server/manage.py \
  ingest_tileset \
  --filename /chromSizes.tsv \
  --datatype chromsizes \
  --filetype chromsizes-tsv \
  --coordSystem myAssembly

If you want gene autocomplete as well, you'll need a gene-annotations beddb file with the same coordSystem as the chromSizes file.

danledinh commented 6 years ago

That did the trick! Thanks again!!!