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.

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