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Trouble using Bioconda packages (lima, isoseq3) with channel conda-forge

Ok I've seen a few people with the same problem but no resolution - I am trying to use lima and isoseq3 packages in bioconda. I've set the channels properly using the --add channels defaults --add channels bioconda --add channels conda-forge --set channel_priority strict and when I check config --show channels I get

-conda-forge 
-bioconda 
-defaults

So, should be good to go. But when I try to install a package, I get a PackagesNotFoundError I am running Python 3.9.13 which Bioconda is supposed to support. Is it worth running an earlier version of python to try to install packages? Or has anyone found a solution to this? Any help is appreciated

bioconda pacbio conda lima python
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updated by Billy Rowell • Billy Rowell • written by josc • josc

What command(s) are you running to install rhe software?

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written by rpolicastro rpolicastro

1 answer

  • What operating system are you using? lima and isoseq3 are only available for linux according to pbbioconda.
  • What version of conda are you running? Admittedly, I'm running an older version (4.11.0), but the command below is working to install this environment.
❯ conda --version
conda 4.11.0

❯ conda create -n test_20221031 -c bioconda -c conda-forge -c defaults lima isoseq3
...
The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    isoseq3-3.8.0              |       h9ee0642_0         1.6 MB  bioconda
    lima-2.6.0                 |       h9ee0642_0         2.4 MB  bioconda
    ------------------------------------------------------------
                                           Total:         4.0 MB

The following NEW packages will be INSTALLED:

  isoseq3            bioconda/linux-64::isoseq3-3.8.0-h9ee0642_0
  lima               bioconda/linux-64::lima-2.6.0-h9ee0642_0
...
done
#
# To activate this environment, use
#
#     $ conda activate test_20221031
#
# To deactivate an active environment, use
#
#     $ conda deactivate

It would help to have: 1) your operating system, operating system version, and conda version 2) the exact conda create or conda install command you used 3) the error message

There's also a support section on the pbbioconda page with more details.

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written by Billy Rowell • Billy Rowell

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