installing Clustalw for Bioperl

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9.7 years ago

Andrea ▴ 60

Hi everyone,

I'm trying to run Clustalw through Bioperl. I have downloaded and installed clustalw for windows, but when I 'm trying to use Bio::Tools::Run::Alignment::Clustalw I have an error that this module is missing?

Any help?

bioperl Perl • 4.3k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Andrea ▴ 60

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What do you get when you run perl -MBio::Tools::Run::Alignment::Clustalw?

Oops... for win should be something like this if I recall correctly: ppm query Bio-Tools-Run-Alignment-Clustalw

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by mxs ▴ 530

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Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (you may need to instal
l the Bio::Tools::Run::Alignment::Clustalw module) (@INC contains: C:/Perl64/sit
e/lib C:/Perl64/lib .).
BEGIN failed--compilation aborted.

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Andrea ▴ 60

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The package is missing! How do I install it?

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Andrea ▴ 60

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ppm install Bio::Tools::Run::Alignment::Clustalw

should do the trick

ADD REPLY • link 9.7 years ago by mxs ▴ 530

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Downloading Kobes packlist...failed 500 Can't connect to theoryx5.uwinnipeg.ca:8
0 (Bad hostname)
ppm install failed: Can't find any package that provides Bio::Tools::Run::Alignm
nt::Clustalw

:(

ADD REPLY • link 9.7 years ago by Andrea ▴ 60

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oh sorry. I think you need the whole BioPerl-Run package

http://www.bioperl.org/wiki/Run_package

ADD REPLY • link 9.7 years ago by mxs ▴ 530

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