This page last modified: Aug 14 2009
keywords:gmod,gbrowse,dependent,files,rpm,how,to,howto,install,help,error,warning,inc,missing,make,dependency,dependencies,require,required description:Fedora 11 additional dependencies for the network install of GMOD Gbrowse. title:Gbrowse installation notes See the prerequisites (URL below). I had to install a few packages to meet the prerequisites, but there were several packages that were also prerequisites or other types of dependencies. After my third attempt at running the netinstall, I had a working Gbrowse installation, in spite of several errors and warnings during the install. I accepted all defaults when prompted. The only config I entered was my Apache document root "/var/www/html". During later installs, I chose the a option for "Install [a]ll optional external modules,..." Using Konsole, I found it helpful to clear the scrollback and reset before starting the netinstall. With scrollback set to unlimited, I ran the netinstall. At the end I saved the output to a file for later forensics. I didn't see a logging option in the netinstall, and the netinstall seems to write to both stdout and stderr, and it requires keyboard input. Normal logging wouldn't work. The "screen" command might have some feature for logging, but Konsole's "Save output" works fine. All the packages below were necessary to quiet warnings or errors during the netinstall. http://gmod.org/wiki/GBrowse_Install_HOWTO http://gmod.org/wiki/GBrowse_Install_HOWTO#Prerequisites wget http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl perl gbrowse_netinstall.pl yum -y install perl-CPAN yum -y install gcc # The GD package was installed, but there was still a failed # dependency. Apparently the Gbrowse dependency is perl-GD and not the # standalone (non-Perl) GD. yum -y install perl-GD # My first attempt to run gbrowse_netinstall.pl failed due to no # LWP/Simple.pm. If the installer has an error similar to # Error: Can't locate LWP/Simple.om in @INC # then use "yum whatprovides" to determine if there is a yum package # that will fix the dependency. You must put * before the path name. # yum whatprovides *LWP/Simple.pm yum -y install perl-libwww-perl # I don't think Authen-DigestMD5 was necessary. Fedora 11 doesn't have # Digest::MD5 as far as I can tell, so I was grasping at straws # here. The cpan Digest::MD5 was later installed by hand. yum -y install perl-Authen-DigestMD5 perl-Text-Shellwords perl-Class-Base yum -y install perl-Archive-Tar # perl-XML-LibXML required by /usr/local/bin/bp_search2gff.pl when # using "--format blastxml". Not all supported formats are documented # in the pod docs. yum -y install perl-XML-LibXML # GraphViz failed during netinstall, but with no error # messages. Installing the cpan GraphViz-2.04 by hand I discovered # that it depends on the GraphViz package. Installing perl-GraphViz # via yum took care of both the Perl package and all dependencies. yum -y install perl-GraphViz yum -y install perl-XML-DOM # The line below did not install Digest::MD5, as far as I can tell. I # suggest trying your install with Digest::MD5, but without the # perl-Authen-DigestMD5, and perl-MD5 packages. Without these two # packages, see if you get warnings about tests not performed due to # no MD5. I had to manually install Digest::MD5 as you'll see # later. As far as I can tell, there is no Fedora rpm for Digest::MD5 yum -y install perl-Authen-DigestMD5 perl-MD5 yum -y install perl-Digest-SHA perl-Digest-SHA1 yum -y install perl-XML-Parser # Install Digest::MD5 by hand. I searched cpan for the most recent # version. Even though the gbrowse install script had errors # installing this, it worked flawlessly when I did it by hand. wget http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.39.tar.gz tar -zxvf Digest-MD5-2.39.tar.gz cd Digest-MD5-2.39 perl Makefile.PL make make test make install