Difference between revisions of "GBrowseInstallation"
From WormBaseWiki
Jump to navigationJump to search(6 intermediate revisions by one other user not shown) | |||
Line 1: | Line 1: | ||
+ | <font style="font-size:15pt"> | ||
Notes on installing Gbrowse in the WormBase environment. | Notes on installing Gbrowse in the WormBase environment. | ||
+ | </font> | ||
+ | =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" | 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=== | |
<pre> | <pre> | ||
# This file is read by Makefile.PL | # This file is read by Makefile.PL | ||
Line 20: | Line 24: | ||
</pre> | </pre> | ||
− | + | ==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 | perl Makefile.pl | ||
− | + | ==Installation== | |
+ | *Do the installation with the incantation below. | ||
sudo make install UNINST=1 | 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. | ||
+ | |||
+ | |||
+ | |||
+ | [[Category:User Guide]] | ||
+ | [[Category:Developer documentation]] |
Latest revision as of 23:10, 13 August 2010
Notes on installing Gbrowse in the WormBase environment.
Contents
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.