BIRCH - Overriding BIRCH
core programs
In some cases you may wish to override programs in the BIRCH core:
- to a more recent version
- to fix a bug in a BIRCH core program
- to replace a BioLegato menu item with one tailored to the
local system
In all cases, BIRCH sets the $local/bin-xxx-xxx directories earlier
in the search $PATH than $birch/bin-xxx-xxx directories. Similarly,
$local/script appears ahead of $BIRCH/script in the $PATH.
Simply place the binary in the appropriate $local directory, and it
will override the BIRCH core program with the same name. The one
caveat is that when BIRCH is upgraded to new version, binaries and
scripts in $local will still supersede those in the core. If a newer
version is now in BIRCH, you may wish to delete your
locally-installed version.
Overriding BioLegato menu
items
This is a very common task, and the method is straightforward:
- add the revised menu item (with the same name as the BIRCH
core item) to the appropriate directory in $local/dat for the
relevant BioLegato instance. For example, to override the
database search menu in $dat/bldna/PCD/Database/BLASTN.blmenu,
add a modified copy of this file to
$local/dat/PCD/Database/BLASTN.blmenu. This menu will replace
the default menu.
These files would have to be edited so that the BioLegato mensu
displayed the names of the actual databases available on your
system.
Please send suggestions of comments
regarding this page to psgendb@cc.umanitoba.ca