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Downloading GRCh38 from Ensembl #254

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avantikalal opened this issue Jan 28, 2025 · 0 comments
Open

Downloading GRCh38 from Ensembl #254

avantikalal opened this issue Jan 28, 2025 · 0 comments

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@avantikalal
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Hi, I'm trying to install GRCh38 from Ensembl using genomepy.install_genome(name='GRCh38', provider='Ensembl') and running into the following error:

---------------------------------------------------------------------------
GenomeDownloadError                       Traceback (most recent call last)
Cell In[15], line 1
----> 1 genomepy.install_genome(name='GRCh38', provider='Ensembl')

File [/opt/conda/lib/python3.11/site-packages/genomepy/functions.py:208](http://localhost:8890/lab/tree/code/cryptic-splicing/opt/conda/lib/python3.11/site-packages/genomepy/functions.py#line=207), in install_genome(name, provider, genomes_dir, localname, mask, keep_alt, regex, invert_match, bgzip, annotation, only_annotation, skip_matching, skip_filter, threads, force, **kwargs)
    206 out_dir = os.path.join(genomes_dir, localname)
    207 genome_file = os.path.join(out_dir, f"{localname}.fa")
--> 208 provider = _provider_selection(name, localname, genomes_dir, provider)
    210 # check which files need to be downloaded
    211 genome_found = _is_genome_dir(out_dir)

File [/opt/conda/lib/python3.11/site-packages/genomepy/functions.py:371](http://localhost:8890/lab/tree/code/cryptic-splicing/opt/conda/lib/python3.11/site-packages/genomepy/functions.py#line=370), in _provider_selection(name, localname, genomes_dir, provider)
    368     if p in ["ensembl", "ucsc", "ncbi"]:
    369         provider = p
--> 371 return _lazy_provider_selection(name, provider)

File [/opt/conda/lib/python3.11/site-packages/genomepy/functions.py:352](http://localhost:8890/lab/tree/code/cryptic-splicing/opt/conda/lib/python3.11/site-packages/genomepy/functions.py#line=351), in _lazy_provider_selection(name, provider)
    349         return p
    351 if len(providers):
--> 352     raise GenomeDownloadError(f"{name} not found on {', '.join(providers)}.")
    353 sys.exit(0)

GenomeDownloadError: GRCh38 not found on Ensembl.

However it works with GRCh37. Am I doing something wrong?

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