weixin_39763033
weixin_39763033
2020-12-02 21:03

Snippy install "Can't locate Bio/SeqIO.pm in @INC

Hello, I installed via miniconda bioconda instructions but installation check came up with this error message. Can you please tell me how to fix this? (PS. I'm very new to this.)

Can't locate Bio/SeqIO.pm in (you may need to install the Bio::SeqIO module) ( contains: /home/sharb/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/sharb/miniconda3/lib/site_perl/5.26.2 /home/sharb/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/sharb/miniconda3/lib/5.26.2 .) at /home/sharb/miniconda3/bin/snippy line 11. BEGIN failed--compilation aborted at /home/sharb/miniconda3/bin/snippy line 11.

Thanks,

该提问来源于开源项目:tseemann/snippy

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19条回答

  • weixin_39763033 weixin_39763033 4月前

    Sweet. 2nd one didn't work - just hung the window, but first one did for 4.0.5. Thanks!

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  • weixin_39656206 weixin_39656206 4月前

    Hi, I just installed 4.2 using Conda and have run into the same issue.

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  • weixin_39614546 weixin_39614546 4月前

    snippy 4.2.3 is now in conda and brew. i am told the channel order has changed in brew now. you might have to do conda install -c conda-forge -c bioconda snippy instead. Make sure you conda update conda and conda update --all too!

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  • weixin_39656206 weixin_39656206 4月前

    Great - a Brew reinstall did the trick but the Conda is still not quite working. Thank you for your help and for making these tools available Torsten, much appreciated.

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  • weixin_39614546 weixin_39614546 4月前

    Conda is in so much flux at the moment it is hard to debug, but we will get there. I think it's a python problem now, the freebayes helper scripts. I will replace them with my own perl ones.

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  • weixin_39988331 weixin_39988331 4月前

    I'm still having problems installing Snippy on MacOS using latest (Bio)Conda. Any ideas? snippy --version Can't locate Bio/SeqIO.pm in (you may need to install the Bio::SeqIO module) ( contains: /Users/nick/miniconda3/envs/metaphylo/bin/../perl5 /Users/nick/miniconda3/envs/metaphylo/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level /Users/nick/miniconda3/envs/metaphylo/lib/perl5/site_perl/5.22.0 /Users/nick/miniconda3/envs/metaphylo/lib/perl5/5.22.0/darwin-thread-multi-2level /Users/nick/miniconda3/envs/metaphylo/lib/perl5/5.22.0 .) at /Users/nick/miniconda3/envs/metaphylo/bin/snippy line 15. BEGIN failed--compilation aborted at /Users/nick/miniconda3/envs/metaphylo/bin/snippy line 15.

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  • weixin_39657444 weixin_39657444 4月前

    Howdy. This issue popped up for me with a conda install as well. I used

    conda update --all
    and still nothing.
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  • weixin_39805720 weixin_39805720 4月前

    I have also just come across this same problem

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  • weixin_39614546 weixin_39614546 4月前

    I did not write the conda package for snippy. Please make a whole new conda env for it and see what happens:

    
    conda activate base
    conda update --all --yes
    conda create -n snippy_env snippy>=4.6
    conda activate snippy_env
    snippy --check
    

    does it work for you now?

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  • weixin_39756416 weixin_39756416 4月前

    I tried the solution you posted 15 days ago after running into the same issue and it did not fix the error. Not sure why but the install from the readme seemed to download a 3.1v originally.

    The command hung on conda create -n snippy_env snippy>=4.6

    Edit:

    I got it working with conda activate base conda update --all --yes conda create -n snippy_env conda activate snippy_env conda install -c conda-forge -c bioconda -c defaults snippy conda list (To check version is above 4) snippy --check

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  • weixin_39656206 weixin_39656206 4月前
    • I had the same issue which resolved when I used this slight fix: conda create -n snippy_env snippy=4.6.0 Snippy has worked fine subsequently.
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  • weixin_39884078 weixin_39884078 4月前

    Same problem here, and new environment, followed by conda install -c conda-forge -c bioconda -c defaults snippy did not solve the problem.

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  • weixin_39729840 weixin_39729840 4月前

    conda install snippy >snippy 3.1 run error github clone snippy>snippy 4.6 run ok here: git clone https://github.com/tseemann/snippy.git

    You'll need to add Snippy's bin directory to your $PATH

    maybe conda snippy is old version not upgrade

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  • weixin_39614546 weixin_39614546 4月前

    I am told bioperl is currently broken on bioconda, and that it will be fixed within a week.

    Snippy 4 will not appear until that is fixed first.

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  • weixin_39763033 weixin_39763033 4月前

    Wow! so fast - thank you. So do I need to undo the install for now and re-install when the fix is done? (if so, how?) And will you post a note to say when it's fixed?

    thanks again.

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  • weixin_39614546 weixin_39614546 4月前

    i think 4.0.0 now works on bioconda. i am not sure how to upgrade it. maybe conda update --all ?

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  • weixin_39763033 weixin_39763033 4月前

    Thanks for that. I used conda update --all and it all went through without a hitch, but still v3.1.

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  • weixin_39614546 weixin_39614546 4月前

    Try

    
    conda install snippy==4.05
    

    or

    
    conda install -c bioconda -c conda-forge snippy>=4.0
    
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  • dream_and_sugar 梦和糖浆 1月前

    I have the same question and use conda update --all. Final I still can't used snippy. Do you have any advice?

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