GBrowseInstallation

Notes on installing Gbrowse in the WormBase environment.

Installing without architecture-specific library paths

One barrier to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GBrowse uses by default. The following recipe gets rid of this "feature"

Checkout

Check out a fresh copy of the 'stable' branch, or run 'make realclean' and do a CVS update. Create or edit the file GGB.def in the same directory as Makefile.PL.

GGB.def

# This file is read by Makefile.PL

CGIBIN=/usr/local/wormbase/cgi-perl/seq
DO_XS=0
APACHE=/usr/local/apache
CONF=/usr/local/wormbase/conf
GBROWSE_ROOT=gbrowse
HTDOCS=/usr/local/wormbase/html
#LIB=/usr/local/wormbase/lib
VERSION=1.69
BIOGRAPHICS_VERSION=1.654

MakeFile.PL

• Run perl Makefile.PL with the usual options plus DO_XS=0.
• You can either edit the GGB.def or use the command line args.
• To contain the perl libraries, you can set the LIB option as well.
• The DO_XS option is why the GBrowse libs have been going into architecture-dependent paths. It concerns a tiny but rarely-used bit C code associated with one of the aligner plugins. It is not used in the wormbase.

 perl Makefile.pl

Installation

• Do the installation with the incantation below.

 sudo make install UNINST=1

• The UNINST=1 should remove the previous installation of libs in the architecture dependent paths but you will want to check to be sure. Manually prune the directory /system/dependent/path/Bio if necessary.
• Check first to make sure bioperl is not installed in there (it should not be).
• If required, you may want to change the ownership and/or permissions of files in the paths described above ig GGB.def

Plugin Notes

PrimerDesigner

The plugin requires:

• the CPAN packages Bio::PrimerDesigner and Class::Base
• the primer3 binary installed in /usr/local/bin. If it has another name, it should be symlinked to 'primer3'.

Spectrogram

• requires Math::FFT, which is an XS module.