GEP header

How to Tweak Consed

If you're getting the three lines of ": Command not found" when you change the shell, it seems that miniassembly doesn't work in Consed, nor does phredPhrap. If you don't need to use either of these commands you can skip this, as Consed otherwise seems to work fine. If you do need to use one, type the following after you get that initial three-lines message (and as always in Unix, note that the spaces are important):

setenv[space]CROSS_MATCH_VECTOR[space]/usr/local/genome/lib/screenLibs/vector.seq

Continue as usual and things should now work properly.