Finesim97/MetaErgInstallHelper

Can't locate Bio/SeqIO.pm in @INC

Closed this issue · 4 comments

s4251484 commented

hi @Finesim97 and team

thanks for creating this helper! my installation was successful, but having problem to run this Perl script. any idea?

(/RDS/Q1034/conda/metaerg) s4251484@tinaroo1:.../MetaErg/metaerg/bin> /RDS/Q2348/MetaErg/metaerg/bin/metaerg.pl
Can't locate Bio/SeqIO.pm in @inc (@inc contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /RDS/Q2348/MetaErg/metaerg/bin/metaerg.pl line 10.
BEGIN failed--compilation aborted at /RDS/Q2348/MetaErg/metaerg/bin/metaerg.pl line 10.

Finesim97 commented

Hi,
It seems like the wrong Perl (System installation, not Conda env) is being used. Metaerg uses the /usr/bin/env command to find it. I am a little bit confused by your paths:
/RDS/Q1034/conda/metaerg: This is the path called metaerginstall in the manual?
/RDS/Q2348/MetaErg/metaerg: Another metaerg installation path?

Could you try in a new session (new terminal/ssh connection):

which perl
conda activate /RDS/Q1034/conda/metaerg
which perl
metaerg.pl

When giving no path, the version installed by the installed will be used. Do you have to use the version in /RDS/Q2348/? Does it contain the reference data, you want to use?

s4251484 commented

Hi,
It seems like the wrong Perl (System installation, not Conda env) is being used. Metaerg uses the /usr/bin/env command to find it. I am a little bit confused by your paths:
/RDS/Q1034/conda/metaerg: This is the path called metaerginstall in the manual?
/RDS/Q2348/MetaErg/metaerg: Another metaerg installation path?

Could you try in a new session (new terminal/ssh connection):

which perl
conda activate /RDS/Q1034/conda/metaerg
which perl
metaerg.pl

When giving no path, the version installed by the installed will be used. Do you have to use the version in /RDS/Q2348/? Does it contain the reference data, you want to use?

hi @Finesim97 thanks for your prompt reply!
below is what I got

which perl
/usr/bin/perl

module load anaconda (I ran this on a cluster, hence module loading)
source activate /RDS/Q1034/conda/metaerg

(/RDS/Q1034/conda/metaerg) s4251484@tinaroo2:~> which perl
/RDS/Q1034/conda/metaerg/bin/perl

yea I have my conda env in this path /RDS/Q1034/conda/metaerg
and /RDS/Q2348/MetaErg/metaerg (supposedly metaerginstall) is where I downloaded the gz files and your script.

Finesim97 commented

Ok,
The script automatically creates a custom Conda environment (stored as metaerginstall according to the Readme), into which metaerg is downloaded and installed into.

Did you create the conda env /RDS/Q1034/conda/metaerg with the script? Did the command (metaerg.pl) without any path print anything?

s4251484 commented

Ok,
The script automatically creates a custom Conda environment (stored as metaerginstall according to the Readme), into which metaerg is downloaded and installed into.

Did you create the conda env /RDS/Q1034/conda/metaerg with the script? Did the command (metaerg.pl) without any path print anything?

yea it is a fix!
sorry I acted smart and created my own conda env! deleted it and activate the conda env which the script created and now my metaerg is working now! thanks!