Open douglasgscofield opened 5 months ago
I should add that to use existing BUSCO v5 lineage sets for compleasm, each of the lineage directories, e.g., methanomicrobia_odb10
, needs a corresponding methanomicrobia_odb10.done
file at the same level, this can be created with touch
for each lineage directory:
cd <BUSCO v5 lineage sets base directory>/lineages
for D in *_odb10; do
test -d $D && touch $D.done
done
Also, if you uncompress the refseq_db.faa.gz
within each lineage directory, leave the gzipped version in place for compleasm to use.
Adds the ability to specify the library path (what is set via
--library_path
) using the environment variableCOMPLEASM_LIBRARY_PATH
. The logic is:--library_path
options wherever they appear toNone
args.library_path == None
, then check if environment variableCOMPLEASM_LIBRARY_PATH
is setargs.library_path
mb_downloads
, which will be in the current directoryThis also modifies the
__init__
logic inDownloader
to do the same.This change enables using a central location for lineage sets, useful for streamlining project-wide storage or, for example, for HPC clusters such as ours where we've already downloaded the lineage sets to the same system-wide location for both BUSCO and compleasm. These lineage sets do not often change, so enabling the use of a common location for them is not just feasible but recommended.