Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

On Tue, 14 Jul 2020, Zhiliang Hu wrote:

> Date: Tue, 14 Jul 2020 10:59:21 -0500 (CDT)
> From: Zhiliang Hu <hu...@an...>
> To: Colin <col...@gm...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
>
> Thanks Colin for addressing the issue.  I took the path to reinstall the 
> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the 
> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>
> My newly downloaded JBrowse setup.sh (at a location different from previous 
> installations; on a RedHat CentOS 7 system) got complains like:
>
> Installing Perl prerequisites ...
> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>
> I understand it might be caused by multiple perl versions on my system but by 
> cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder is 
> there alternative ways to install "Bio::Perl@1.7.2" (actually which 
> modules?).
>
> I searched for old JBrowse troubleshooting and did:
>> sudo yum groupinstall "Development Tools"
>> sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
> and it didn't help.
>
> Any further suggestion please? (I know on this RH Centos7 system there are 
> perl GD, Zlib, and libpng installed but how to make the JBrowse setup know 
> where they are?)

By the way I did rm -rf ~/.cpanm and ~/.cpan, but don't know how to remove 
"extlib".  I also did 'install JSON::XS' with cpan.

Zhiliang