The scripts to run the de novo assembly stuff are in src in the bpipe and old_bpipe directories. These were done before we settled on a pipeline setup, so they are a bit of a mess. They will one day be ported over to the new pipeline. These won’t be functional without some massaging and are there as legacy to keep track of which parameters we used for everything.
The scripts to perform the blastn annotation use the new pipeline. Those are in the scripts subdirectory and are runnable assuming ipython, bcbio and rkinf is installed.