The way to do this was:

1) Download and install sparsehash (see abyss documentation) in abyss/sparsehash.

2) ./configure --prefix=$BIRCH/lib-$BIRCH_PLATFORM/abyss CPPFLAGS=-I$BIRCH/install/abyss-master/sparsehash/src

3) make

4) make install


5) Then, we get the following message when trying to run abyss-pe:

zsh: no such option: pipefail

Had to create $BIRCH/script/zsh,  a wrapper to run locally-installed copy of zsh.
This script sets the LD_LIBRARY_PATH to read libraries from $BIRCH/lib-$BIRCH_PLATFORM/zsh-5.5.1,
and then runs $BIRCH/bin-$BIRCH_PLATFORM/zsh.

Finally, abyss-pe has to be edited to use $BIRCH/script/zsh, rather than the system zsh.

Grepping through the other abyss scripts shows that only abyss-pe calls zsh.