Difference between revisions of "GBrowseInstallation"
(New page: Notes on installing Gbrowse in the WormBase environment. One barrier to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GB...) |
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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" | 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" | ||
− | 1) Check out a fresh copy of the 'stable' branch, or run 'make realclean' and do a CVS update. | + | 1) 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''' | '''GGB.def''' | ||
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2) 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. | 2) 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 | + | |
− | 3) Do the installation with the incantation below. | + | perl Makefile.pl |
+ | |||
+ | 3) Do the installation with the incantation below. | ||
+ | |||
sudo make install UNINST=1 | sudo make install UNINST=1 | ||
+ | |||
+ | 4) 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). |
Revision as of 07:45, 14 February 2008
Notes on installing Gbrowse in the WormBase environment.
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"
1) 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
2) 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
3) Do the installation with the incantation below.
sudo make install UNINST=1
4) 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).