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edta-2.2.2 is incompatible with LTR_FINDER_parallel in conda/mamba install #526

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drk0311 opened this issue Dec 10, 2024 · 1 comment
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@drk0311
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drk0311 commented Dec 10, 2024

I installed EDTA-2.2.2 via mamba and encountered an error message saying LTR_FINDER_parallel cannot be installed because of incompatibility with edta-2.2.2.

The error message was as below.

ClobberError: This transaction has incompatible packages due to a shared path.
   packages: bioconda/noarch::ltr_finder_parallel-1.1-hdfd78af_1, bioconda/noarch::edta-2.2.2-hdfd78af_0
   path: 'bin/LTR_FINDER_parallel

After installation is finished, there is a binary file of LTR_FINDER_parallel but nothing in ~/miniforge3/envs/EDTA/share/EDTA/bin/.
So when I try to execute LTR_FINDER_parallel, it says

Can't open perl script "/home/naitok785/miniforge3/envs/test/share/EDTA/bin/LTR_FINDER_parallel/LTR_FINDER_parallel": No such file or directory

I managed to have EDTA work by removing the LTR_FINDER_parallel binary form the ~/miniforge3/envs/EDTA/bin, git cloned LTR_FINDER_parallel myself and soft-linked the cloned binary and bin directory to the ~/miniforge3/envs/EDTA/bin, as like

cd ~/miniforge3/envs/EDTA/bin
ln -s ~/LTR_FINDER_parallel/LTR_FINDER_parallel .
ln -s ~/LTR_FINDER_paralle/bin .

Thank you anyway, I have been a long-time user of this fantastic pipeline!

@oushujun
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There were two bugs in here, we have just updated the recipe to fix them both. Please try again. Thanks!

Shujun

@oushujun oushujun added the bug Something isn't working label Dec 16, 2024
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