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I used Ubuntu 18.04 LTS for Windows from Microsoft store and tried to install BioPerl module Bio::SeqIO with cpanm Bio::SeqIO. Perl version is v5.26.1. It seems that module installation failed:

! Installing the dependencies failed: Module 'XML::Twig' is not installed, Module 'XML::LibXNL::Reader' is not installed, Module 'XML::LibXML' is not installed, Module 'XML::Parser::PerlSAX' is not installed, Module 'XML::DOM::XPath' is not installed, Module 'XML::DOM' is not installed
! Bailing out the installation for BioPerl-1.7.7
58 distributions installed

If i run a script with line use Bio::SeqIO; I get an error:

    Can't locate Bio/SeqIO.pm in @INC (you may need to install the 
        Bio::SeqIO module) (@INC contains: ...

I am not sure how to proceed. I could try to install dependencies that failed with cpanm but I do not know if it is a proper way.

zubenel
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    What happens when you try to install XML::Twig (as noted in the first error message)? – brian d foy Jan 13 '20 at 20:05
  • I get failure with dependencies: `Found dependencies: XML::Parser --> Working on XML::Parser ... ! Configure failed for XML-Parser-2.46. ! Installing the dependencies failed: Module 'XML::Parser' is not installed` – zubenel Jan 13 '20 at 20:18
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    It sounds like you need to install expat, the external library that XML::Parser needs – brian d foy Jan 14 '20 at 03:49

2 Answers2

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I tried this on my Windows 10 laptop:

  • Installed WSL Ubuntu 18.10 as described here, then

  • Using the system perl, i.e /usr/bin/perl (maybe it would have been better to use perlbrew and installed a custom perl and such avoid using sudo) from the Linux terminal window:

    sudo apt-get update
sudo apt-get -y install make gcc libexpat1-dev
sudo cpan local::lib
sudo cpan App::cpanminus
sudo cpanm -n Time::Zone  # <-- failed tests
sudo cpanm -n XML::DOM::XPath # <-- failed tests
sudo cpanm Bio::SeqIO

This worked for me.

Håkon Hægland
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Perhaps sudo apt-get install bioperl bioperl-run would install all modules which you might need in feature.

Bioperl

Andrew
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