Re: [Gmod-ajax] Perl lib version question

[Colin <col...@gm...>]

The "extlib" folder is inside of the jbrowse folder


-Colin

On Tue, Jul 14, 2020 at 1:04 PM Zhiliang Hu <hu...@an...> wrote:

> 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
>