OSError: Installing gene annotations requires missing UCSC tools. See https://github.com/vanheeringen-lab/genomepy#pip for download links and details.

[allankamau]

I have installed genomepy. I have the following software installed in my /usr/local/bin directory

genePredToBed
genePredToGtf
bedToGenePred
gtfToGenePred
gff3ToGenePred

I am running the command below but I get an error message advising that UCSC tools are missing.

genomepy install xenTro9 --UCSC-annotation refGene

Below is the full output.

root@567b7019ab11:/local/data/nf_genome_annot_backend# genomepy install xenTro9 --UCSC-annotation refGene
04:42:12 | INFO | Downloading genome from UCSC. Target URL: https://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/bigZips/xenTro9.fa.gz...
Download: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 419M/419M [24:45<00:00, 296kB/s]
05:06:58 | INFO | Genome download successful, starting post processing...
05:07:05 | INFO | name: xenTro9
05:07:05 | INFO | local name: xenTro9
05:07:05 | INFO | fasta: /root/.local/share/genomes/xenTro9/xenTro9.fa
Filtering Fasta: 28.8M lines [00:14, 2.00M lines/s]
05:08:00 | INFO | Downloading the refGene annotation from the UCSC MySQL database.
Traceback (most recent call last):
  File "/usr/local/lib/python3.13/site-packages/genomepy/providers/ucsc.py", line 343, in download_annotation
    download_annotation(name, annot, genomes_dir, localname)
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/genomepy/providers/ucsc.py", line 549, in download_annotation
    check_ucsc_tools()
    ~~~~~~~~~~~~~~~~^^
  File "/usr/local/lib/python3.13/site-packages/genomepy/utils.py", line 179, in check_ucsc_tools
    raise OSError(
    ...<3 lines>...
    )
OSError: Installing gene annotations requires missing UCSC tools. See https://github.com/vanheeringen-lab/genomepy#pip for download links and details.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/genomepy", line 8, in <module>
    sys.exit(cli())
             ~~~^^
  File "/usr/local/lib/python3.13/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.13/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.13/site-packages/genomepy/cli.py", line 262, in install
    genomepy.install_genome(
    ~~~~~~~~~~~~~~~~~~~~~~~^
        name,
        ^^^^^
    ...<14 lines>...
        **kwargs,
        ^^^^^^^^^
    )
    ^
  File "/usr/local/lib/python3.13/site-packages/genomepy/functions.py", line 264, in install_genome
    provider.download_annotation(name, genomes_dir, localname=localname, **kwargs)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/genomepy/providers/ucsc.py", line 346, in download_annotation
    raise GenomeDownloadError(
    ...<4 lines>...
    )
genomepy.exceptions.GenomeDownloadError: An error occured while installing the gene annotation for xenTro9 from UCSC.
If you think the annotation should be there, please file a bug report at: https://github.com/vanheeringen-lab/genomepy/issues

Error: Installing gene annotations requires missing UCSC tools. See https://github.com/vanheeringen-lab/genomepy#pip for download links and details.