Difference between revisions of "GBrowseInstallation"

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Notes on installing Gbrowse in the WormBase environment.
 
Notes on installing Gbrowse in the WormBase environment.
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=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"
  
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.
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==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'''
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===GGB.def===
 
<pre>
 
<pre>
 
# This file is read by Makefile.PL
 
# This file is read by Makefile.PL
Line 20: Line 24:
 
</pre>
 
</pre>
  
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.
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==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
  
3) Do the installation with the incantation below.   
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==Installation==
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*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).
+
* 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]]
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[[Category:Developer documentation]]

Latest revision as of 23:10, 13 August 2010

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.