[Gmod-gbrowse] gbrowse_syn install on ubuntu16.04

[kentnf .]

Hello,

I install the latest version of Gbrowse following this document (
http://gmod.org/wiki/GBrowse_syn_Tutorial). It works well on Fedora server,
but not on ubuntu 16.04 (production server). When I check the apache log
file, there are 4 records:

gbrowse_syn: Subroutine main::start_html redefined at
/usr/share/perl/5.22/Exporter.pm line 66.: /var/www/cgi-bin/gb2/gbrowse_syn

DataSource.pm: Unescaped left brace in regex is deprecated, passed through
in regex; marked by <-- HERE in m/\\$ENV{ <-- HERE (\\S+)}/ at
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/Graphics/Browser2/DataSource.pm
line 955, <DATA> line 192.: /var/www/cgi-bin/gb2/gbrowse_syn

Util.pm: Subroutine Legacy::Graphics::Browser::Util::start_html redefined
at /usr/share/perl/5.22/Exporter.pm line 66.:
/var/www/cgi-bin/gb2/gbrowse_syn

Synteny.pm: Subroutine Legacy::Graphics::Browser::Synteny::start_html
redefined at /usr/share/perl/5.22/Exporter.pm line 66.:
/var/www/cgi-bin/gb2/gbrowse_syn

When I install the Gbrowse, I use apt-get at first. Then I noticed the
apt-get may not install the last version of Gbrowse. So I install it again
follow the Tutorial (http://gmod.org/wiki/GBrowse_syn_Tutorial).

How can I set up the gbrowse_syn correctly? Thanks for you help.



Best,
Yi Zheng
BTI

[Scott Cain]

Hello Yi Zheng,

I wonder if this is due to different perl versions. Can you do "perl -v"
on each machine and report back the first line of the results (where it
gives the version)?

Thanks,
Scott

Post by kentnf .
Hello,
I install the latest version of Gbrowse following this document (
http://gmod.org/wiki/GBrowse_syn_Tutorial). It works well on Fedora
server, but not on ubuntu 16.04 (production server). When I check the
gbrowse_syn: Subroutine main::start_html redefined at
/usr/share/perl/5.22/Exporter.pm line 66.: /var/www/cgi-bin/gb2/gbrowse_
syn
DataSource.pm: Unescaped left brace in regex is deprecated, passed through
in regex; marked by <-- HERE in m/\\$ENV{ <-- HERE (\\S+)}/ at
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/Graphics/Browser2/DataSource.pm
line 955, <DATA> line 192.: /var/www/cgi-bin/gb2/gbrowse_syn
Util.pm: Subroutine Legacy::Graphics::Browser::Util::start_html redefined
/var/www/cgi-bin/gb2/gbrowse_syn
Synteny.pm: Subroutine Legacy::Graphics::Browser::Synteny::start_html
/var/www/cgi-bin/gb2/gbrowse_syn
When I install the Gbrowse, I use apt-get at first. Then I noticed the
apt-get may not install the last version of Gbrowse. So I install it again
follow the Tutorial (http://gmod.org/wiki/GBrowse_syn_Tutorial).
How can I set up the gbrowse_syn correctly? Thanks for you help.
Best,
Yi Zheng
BTI
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