GBrowse Installation Problem

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GBrowse Installation Problem

weidmao
Hi all,
   I failed the test after the installation of GBrowse and received the
error message, part of them are:

# stderr: Can't locate Bio/Graphics.pm in @INC (@INC contains:
/home/weidongmao/GBrowse/blib/lib /home/weidongmao/GBrowse/blib/arch
/home/weidongmao/GBrowse/install_util /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
/home/weidongmao/GBrowse/blib/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
line 5.
# BEGIN failed--compilation aborted at
/home/weidongmao/GBrowse/blib/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
line 5.
*use Bio::Graphics 2.24 (line 5 from AuthorizedFeatureFile.pm) ;*
# Compilation failed in require at (eval 2) line 3.
#       ...propagated at /usr/share/perl5/base.pm line 94.
# BEGIN failed--compilation aborted at
/home/weidongmao/GBrowse/blib/lib/Bio/Graphics/Browser2.pm line 9.
*use base 'Bio::Graphics::Browser2::AuthorizedFeatureFile';  (line 9 from
Browser2.pm)*
# Compilation failed in require at cgi-bin/das line 20.
# BEGIN failed--compilation aborted at cgi-bin/das line 20.

Need helps on this issue, thanks a lot

Weidong
 
   



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Re: GBrowse Installation Problem

Scott Cain
Hi Weidong,

Perl thinks that you didn't install Bio::Graphics (a GBrowse prerequisite) yet.  Did it install?  The most frequent hang up that causes the installation of Bio::Graphcs to fail is not having libgd and GD.pm installed.

Scott



On Thu, Feb 6, 2014 at 8:12 AM, weidmao <[hidden email]> wrote:
Hi all,
   I failed the test after the installation of GBrowse and received the
error message, part of them are:

# stderr: Can't locate Bio/Graphics.pm in @INC (@INC contains:
/home/weidongmao/GBrowse/blib/lib /home/weidongmao/GBrowse/blib/arch
/home/weidongmao/GBrowse/install_util /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
/home/weidongmao/GBrowse/blib/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
line 5.
# BEGIN failed--compilation aborted at
/home/weidongmao/GBrowse/blib/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
line 5.
*use Bio::Graphics 2.24 (line 5 from AuthorizedFeatureFile.pm) ;*
# Compilation failed in require at (eval 2) line 3.
#       ...propagated at /usr/share/perl5/base.pm line 94.
# BEGIN failed--compilation aborted at
/home/weidongmao/GBrowse/blib/lib/Bio/Graphics/Browser2.pm line 9.
*use base 'Bio::Graphics::Browser2::AuthorizedFeatureFile';  (line 9 from
Browser2.pm)*
# Compilation failed in require at cgi-bin/das line 20.
# BEGIN failed--compilation aborted at cgi-bin/das line 20.

Need helps on this issue, thanks a lot

Weidong





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Re: GBrowse Installation Problem

weidmao
Scott, looks like the libgd was installed when I check the system using "rpm
-qa | grep gd", see following

gupnp-igd-0.1.3-3.1.el6.x86_64
gdm-plugin-fingerprint-2.30.4-52.el6.x86_64
gd-2.0.35-11.el6.x86_64
libgdata-0.6.4-2.el6.x86_64
pulseaudio-gdm-hooks-0.9.21-14.el6_3.x86_64
gdbm-devel-1.8.0-36.el6.x86_64
php-gd-5.3.3-27.el6_5.x86_64
plymouth-gdm-hooks-0.8.3-27.el6.centos.x86_64
eggdbus-0.6-3.el6.x86_64
gdbm-1.8.0-36.el6.x86_64
gdm-user-switch-applet-2.30.4-52.el6.x86_64
gdm-libs-2.30.4-52.el6.x86_64
gdm-2.30.4-52.el6.x86_64
gdb-7.2-60.el6_4.1.x86_64

Do you know what's going on here? Thanks.




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Re: GBrowse Installation Problem

Scott Cain
You probably need either the gd-devel package, or what would probably be easier, is the perl-GD package.  The perl-GD packages provides GD.pm, which is the prerequisite for Bio::Graphics.

Scott



On Fri, Mar 14, 2014 at 11:32 AM, weidmao <[hidden email]> wrote:
Scott, looks like the libgd was installed when I check the system using "rpm
-qa | grep gd", see following

gupnp-igd-0.1.3-3.1.el6.x86_64
gdm-plugin-fingerprint-2.30.4-52.el6.x86_64
gd-2.0.35-11.el6.x86_64
libgdata-0.6.4-2.el6.x86_64
pulseaudio-gdm-hooks-0.9.21-14.el6_3.x86_64
gdbm-devel-1.8.0-36.el6.x86_64
php-gd-5.3.3-27.el6_5.x86_64
plymouth-gdm-hooks-0.8.3-27.el6.centos.x86_64
eggdbus-0.6-3.el6.x86_64
gdbm-1.8.0-36.el6.x86_64
gdm-user-switch-applet-2.30.4-52.el6.x86_64
gdm-libs-2.30.4-52.el6.x86_64
gdm-2.30.4-52.el6.x86_64
gdb-7.2-60.el6_4.1.x86_64

Do you know what's going on here? Thanks.




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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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applications. Written by three acclaimed leaders in the field,
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http://p.sf.net/sfu/13534_NeoTech
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