Eliza,
I'm still suspicious about the $PWD thing. If you're running 'make'
normally, you might try something like
$ PWD=$(pwd) make ...
instead of just
$ make ...
to see whether that improves your situation. Alternatively, for the
'root' steps, you could do something like
$
We basically tried that already: Eliza says the suggested
export PWD=/opt/trans_proteomic_pipeline/src ; make all install
did not work. She also tried the SRC_ROOT= $(shell pwd) change to the
makefile. There's something deeper going on.
Eliza, what shell do you use? I do see from googling
