Perl modules not recognized-CodePudding

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).

CodePudding user response：

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

CodePudding user response：

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.