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 GDE 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 GDE 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/GDE/makemenus/menus.
Add an entry to the $local/dat/GDE/makemenus/menulist file
re-run customdoc.py

For example, if you had a locally-installed BLAST database, and wanted to override the NCBI Blast that comes with the BIRCH core GDE menus, you could install revised BLAST.item files in $local/dat/GDE/makemenus/menus/Database. These files would have to be edited so that the GDE mensu displayed the names of the actual databases available on your system. Examples of GDE menu item files that could be used for locally-installed BLAST and FASTA database searches can be found in $BIRCH/local-generic/dat/GDE/makemenus/menus/Database.

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