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LANL-Bioinformatics / PhaME

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
GNU General Public License v3.0
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Can't locate Bio/SeqIO.pm in @INC #13

Open gpmoran opened 3 years ago

gpmoran commented 3 years ago

So I have installed phame and the dependencies separately in a new environment and installed phame by cloning the github version, as recommended in another thread. When I run the TestAll.sh I get an error that it can't locate Bio/SeqIO.pm in @INC. I think this should have been installed with bioPerl so I am not sure why it cannot locate it?

(my_env) Garys-MacBook-Pro:PhaME garymoran$ test/TestAll.sh 1 Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /Users/garymoran/PhaME/src/../ext/lib/perl5 /Users/garymoran/PhaME/src/../lib /Users/garymoran/PhaME/src /Users/garymoran/miniconda2/envs/my_env/lib/site_perl/5.26.2/darwin-thread-multi-2level /Users/garymoran/miniconda2/envs/my_env/lib/site_perl/5.26.2 /Users/garymoran/miniconda2/envs/my_env/lib/5.26.2/darwin-thread-multi-2level /Users/garymoran/miniconda2/envs/my_env/lib/5.26.2 .) at src/phame line 16. BEGIN failed--compilation aborted at src/phame line 16.

Thanks for any suggested solutions!

drish91 commented 3 years ago

I was running into a similar issue and updating the PERL5LIB env path with the perl5 libs under the phame_env installation path fixed this. This should add the necessary perl libraries in your @INC.

export PERL5LIB="/path/for/anaconda3/envs/phame_new/lib/perl5/site_perl/5.22.0"

gpmoran commented 3 years ago

Thank you, this has solved the issue for me!