Difficulty installing Bioperl for use with GUIDANCE

Question

[alicecol]

Hi,

I am trying to use the Guidance software to analyze a set of 427 sequences. I have the software downloaded and installed the modules indicated in the Guidance user guide (Perl/BioPerl/Ruby), but when I attempt to run Guidance with the following command:

perl /project/thrash_425/alicecol/phylo/guidance.v2.02/www/Guidance/guidance.pl --seqFile bt_coi.fasta --msaProgram MUSCLE --seqType nuc --outDir /project/thrash_425/alicecol/phylo/data/gdtest

I get this error*:

Can't locate Bio/Perl.pm in @INC (you may need to install the Bio::Perl module) (@INC contains: /project/thrash_425/alicecol/phylo/guidance.v2.02/www/Guidance/../Selecton/ 

*truncated for readability

Using cpanm to install Bio::Perl has been unsuccessful, returning the error:

    Can't write to /spack/apps/linux-centos7-x86_64/gcc-8.3.0/perl-5.30.1-hrnelgolwrunau5sesq3phgccj5uqy3h/lib/site_perl/5.30.1 and /spack/apps/linux-centos7-x86_64/gcc-8.3.0/perl-5.30.1-hrnelgolwrunau5sesq3phgccj5uqy3h/bin: Installing modules to /home1/alicecol/perl5
! To turn off this warning, you have to do one of the following:
!   - run me as a root or with --sudo option (to install to /spack/apps/linux-centos7-x86_64/gcc-8.3.0/perl-5.30.1-hrnelgolwrunau5sesq3phgccj5uqy3h/lib/site_perl/5.30.1 and /spack/apps/linux-centos7-x86_64/gcc-8.3.0/perl-5.30.1-hrnelgolwrunau5sesq3phgccj5uqy3h/bin)
!   - Configure local::lib in your existing shell to set PERL_MM_OPT etc.
!   - Install local::lib by running the following commands
!
!         cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
!
! Finding Bio::Perl on cpanmetadb failed.
! Finding Bio::Perl () on mirror http://www.cpan.org failed.
! Couldn't find module or a distribution Bio::Perl

Should I be going about downloading Bioperl a different way?

[Arup Ghosh]

As mentioned in the error message, cpanm is unable to write files in default Perl library path. Either run cpanm as root or install in local library path(~/perl5).

[cardon.chc]

Hi,

Did you solve this problem? I am having the same problem. I have the same message error but when I run cpanm Bio::Perl show a message error but also show that I already have the Perl module installed.

Can't write to /usr/local/share/perl/5.30.0 and /usr/local/bin: Installing modules to /home/cardon05/perl5
! To turn off this warning, you have to do one of the following:
!   - run me as a root or with --sudo option (to install to /usr/local/share/perl/5.30.0 and /usr/local/bin)
!   - Configure local::lib in your existing shell to set PERL_MM_OPT etc.
!   - Install local::lib by running the following commands
!
!         cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
!
Bio::Perl is up to date. (1.7.4)

[Arup Ghosh]

The solution is in the error message itself. The user does not have write permission in usr/local/share/perl/5.30.0 and /usr/local/bin. Either install the module as root or install it in user's perl library path.