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How to install Bioperl on Ubuntu 18.x

I am trying to install bioperl on my Ubuntu 18 machine. I ran the following lines of code as suggested by https://zoomadmin.com/HowToInstall/UbuntuPackage/bioperl

sudo apt-get update -y
sudo apt-get install -y bioperl

I tried to run a simple fasta analyzing perl program which has the following bioperl referencing line

 #!/usr/bin/perl -w 
 use strict;
 use Bio::SeqIO;

When I ran it I am getting this error:

perl AnalyzeFasta.pl

Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains:
/home/nadarajan/miniconda3/envs/bioinfo/lib/site_perl/5.26.2/x86_64-linux-thread-multi
/home/nadarajan/miniconda3/envs/bioinfo/lib/site_perl/5.26.2
/home/nadarajan/miniconda3/envs/bioinfo/lib/5.26.2/x86_64-linux-thread-multi
/home/nadarajan/miniconda3/envs/bioinfo/lib/5.26.2 .) at
AnalyzeFasta.pl line 3.
BEGIN failed--compilation aborted at AnalyzeFasta.pl line 3.

Thanks.

bioperl
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updated by h.mon h.mon • written by nadarajan_v • nadarajan_v

1 answer

Install BioPerl with conda.

You are using a conda installed Perl, and installing BioPerl with the operating system package manager - the conda Perl is not aware of the system-wide Perl packages.

• 0 views • link
written by h.mon h.mon

Please let me know how to install Bioperl on conda installed Perl. Thanks

• 0 views • link
written by nadarajan_v • nadarajan_v

Thank you so much. That fixed the issue!

• 0 views • link
written by nadarajan_v • nadarajan_v

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