Perl modules not recognized - perl

Question

I'm trying to run unitas_1.7.8.pl, a bioinformatic software available here. Importantly, I've used this software many times in the past successfully on this ubuntu machine. Now when I run the command
perl ~/scripts/unitas_1.7.0.pl -threads 24 -s homo_sapiens -i PCR_Primer_11_S11_L001_R1_001.trim.lng ...
I get the error
Perl module LWP::Simple is not installed on this machine!
Perl module Archive::Extract (in core since 2007-07-07) is not installed on this machine!
Perl modules are available for download at http://www.cpan.org/
If you have CPAN installed try the following:
cpan
install Archive::Extract
exit
If you are on MAC or UNIX you should run cpan with sudo:
sudo cpan
install Archive::Extract
exit
I've followed those instructions and updated AND reinstalled cpan (even though I know it should be fine) without apparent issues. The only thing I can think of that has changed since the last time I successfully used unitas is that the server was hard-rebooted a month ago.
Details:
Distributor ID: Ubuntu
Description: Ubuntu 20.04.2 LTS
Release: 20.04
Codename: focal
$ cpan --version
Loading internal logger. Log::Log4perl recommended for better logging
/home/user/miniconda3/bin/cpan version 1.64 calling Getopt::Std::getopts (version 1.12 [paranoid]),
running under Perl version 5.30.3.
[Now continuing due to backward compatibility and excessive paranoia.
See 'perldoc Getopt::Std' about $Getopt::Std::STANDARD_HELP_VERSION.]
Nothing to install!
$ type -p perl; perl -M5.010 -e'say "$_: $ENV{$_}" for sort grep /^PERL/, keys(%ENV)'; echo 'o conf' | cpan
/home/stewart/miniconda3/bin/perl
[...]
make [/usr/bin/make]
make_arg []
make_install_arg []
make_install_make_command [/usr/bin/make]
makepl_arg [INSTALLDIRS=site]
mbuild_arg []
mbuild_install_arg []
mbuild_install_build_command [./Build]
mbuildpl_arg [--installdirs site]
[...]
$ perl -MLWP::Simple -E 'say $INC{"LWP/Simple.pm"}'
Can't locate LWP/Simple.pm in #INC (you may need to install the LWP::Simple module) (#INC contains: /home/stewart/miniconda3/lib/site_perl/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/site_perl/5.30.3 /home/stewart/miniconda3/lib/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/5.30.3 .).
BEGIN failed--compilation aborted.
$ head -n 1 "$( type -p cpan )"
#!/home/stewart/miniconda3/bin/perl
$ perl -MLWP::Simple -e'print "ok\n"'
Can't locate LWP/Simple.pm in #INC (you may need to install the LWP::Simple module) (#INC contains: /home/stewart/miniconda3/lib/site_perl/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/site_perl/5.30.3 /home/stewart/miniconda3/lib/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/5.30.3 .).
BEGIN failed--compilation aborted.
current state of LWP::Simple and Archive::Extract
$ sudo cpan install LWP::Simple
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/root/.cpan/Metadata'
Database was generated on Tue, 07 Sep 2021 08:55:47 GMT
LWP::Simple is up to date (6.56).
$ sudo cpan install Archive::Extract
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/root/.cpan/Metadata'
Database was generated on Tue, 07 Sep 2021 08:55:47 GMT
Archive::Extract is up to date (0.88).
$ sudo cpan LWP::Simple
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/root/.cpan/Metadata'
Database was generated on Tue, 07 Sep 2021 08:55:47 GMT
LWP::Simple is up to date (6.56).

Answer 1

If you already have Miniconda, then you should install using the Bioconda channel in an isolated environment. Your Perl installation, from conda, is interfering with your system CPAN modules:
conda create -n unitas -c bioconda unitas
conda activate unitas
unitas.pl -threads 24 -s homo_sapiens -i PCR_Primer_11_S11_L001_R1_001.trim.lng ...
conda deactivate

Answer 2

None of the solutions suggested worked for me except calling perl directly from another directory (which already had it installed).
/usr/bin/perl5.30.0 ~/scripts/unitas_1.7.0.pl ...
There may be a way to switch the default perl used when called to this directory with $PATH, but I found this workaround for now. Thanks all for your help.