Can't locate Bio/SeqIO.pm - path error?
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Entering edit mode
7 days ago
blur ▴ 210

Hi,

I am trying to run snippy on my UBUNTU18 (inside a conda env that has this tool installed) but am getting an error:

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

I checked the posts here, and tried therefore to install BioPerl using:

sudo apt install bioperl

-> bioperl is already the newest version (1.7.2.-2)

Then I tried: cpnam Bio::Perl

--> I get multiple "bailing" errors...

I think (I might be wrong) that there is something off with my path but I can't figure out what it is. the path reads:

/home/anaconda3/env/snippy/lib/site_perl/5.26.2/x86_64-linux-thread-multi 

Any help would be greatly appreciated,

bioperl • 147 views
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3
Entering edit mode
6 days ago

From what you've posted, it looks like that you are running into the problem of installing system packages vs. conda packages. The BioPerl will likely be available for the system's perl after the apt get, not for the conda one.

Check my configuration as an example of the different perl executables:

# normal system perl
xx@xx:~$ which perl
/usr/bin/perl
xx@xx:~$ perl -e 'use BioPerl;'

# conda's perl
(env) xx@xx:~$ which perl
/home/xx/miniconda3/envs/env/bin/perl
(env) xx@xx:~$ 
(env) xx@xx:~$ perl -e 'use BioPerl;'
Can't locate BioPerl.pm in @INC ..............

Assuming that the program you are trying to run is installed via conda, and it's calling the perl associated with conda, then you would need to install the BioPerl for the "conda perl".

Check this conda package https://anaconda.org/bioconda/perl-bioperl.

Other things may be broken, but without you checking for what is used when, I cannot help further.

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Entering edit mode

I tried that too - I opened the env where snippy is installed and ran

conda install -c bioconda perl-bioperl

I get a msg: "All requested packages are already installed"

Then I ran: which perl

/home/anaconda3/envs/snippy_env/perl

then I ran snippy to get the same error msg. "Can't locate BioPerl.pm in @INC"

But I did manage to fix it, using your idea - I opened a new env for snippy and installed both bio-perl and snippy from bioconda directly and now it works! so thank you!

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