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"
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.
# 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
- 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.
- 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
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'.
- requires Math::FFT, which is an XS module.