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Species not found error

See original GitHub issue

Hi,

I’m trying to download the zebrafish ensembl data, but I get an error. When I type:

pyensembl install --release 92 --species danio_rerio

I get:

ValueError: Species not found: danio_rerio

If I check the ensmbl ftp server the data is of course there: ftp://ftp.ensembl.org/pub/release-92/gtf/danio_rerio/

If there is no easy fix for this, is there a way to download the data manually and put it into the database?

Thanks! Adrian.

Issue Analytics

State:
Created 5 years ago
Comments:13 (6 by maintainers)

Top GitHub Comments

1reaction

iskandrcommented, Apr 12, 2022

The CLI addition of species never happened and pyensembl has been only lightly maintained since I moved to UNC. I’m starting to work on the OpenVax stack again and just merged a PR increasing the number of species supported.

Which one did you need again?

0reactions

alanwiltercommented, Apr 13, 2022

Thanks for that.

These are the species we are looking for:

GENOMES:
  - 'Homo sapiens [GRCh38]'
  - 'Mus musculus [GRCm39]'
  - 'Rattus norvegicus [mRatBN7]'
  - 'Danio rerio [GRCz11]'
  - 'Drosophila melanogaster [BDGP6]'

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