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

[BjoerlingTaul]

$ snippy Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/taobilin/miniconda3/bin/../perl5 /home/taobilin/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/taobilin/miniconda3/lib/site_perl/5.26.2 /home/taobilin/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/taobilin/miniconda3/lib/5.26.2 .) at /home/taobilin/miniconda3/bin/snippy line 15. BEGIN failed--compilation aborted at /home/taobilin/miniconda3/bin/snippy line 15.

[apetkau]

You will likely want to install snippy to it's own conda environment to avoid Perl dependency mismatches, e.g.,:

conda create --name snippy snippy
conda activate snippy

Alternatively, I've found this issue comes up because there is a mismatch between the version of Perl Bio::SeqIO is installed for and the version available in your particular conda environment. You can find where Bio::SeqIO is installed with find /home/taobilin/miniconda3/ -iname 'Bio'. For example:

find /home/apetkau/miniconda3/envs/snippy -iname 'Bio'
/home/apetkau/miniconda3/envs/snippy/lib/site_perl/5.26.2/Bio
/home/apetkau/miniconda3/envs/snippy/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/Bio
/home/apetkau/miniconda3/envs/snippy/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Bio

Now, you just have to make sure the version of Perl where Bio is installed (in this case 5.26.2) corresponds to the version of Perl available, e.g.,

perl --version

This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

If these don't match you will have to install a new version of Perl in conda (or a different version of Bio::SeqIO).

However, the cleaner solution is still the first one, mainly installing snippy to a separate conda environment.

[BjoerlingTaul]

Thanks for your kindnss.