[2024.8.29] - Added VERSION file created in download_databases.sh
[2024.7.11] - Alignment fraction threshold for genome clustering only applied to reference but should also apply to query. Added --af_mode with either relaxed = max([Alignment_fraction_ref, Alignment_fraction_query]) > minimum_af or strict = (Alignment_fraction_ref > minimum_af) & (Alignment_fraction_query > minimum_af) to edgelist_to_clusters.py, global_clustering.py, local_clustering.py, and cluster.py.
[2024.7.3] - Added pigz to VEBA-annotate_env which isn't a problem with most conda installations but needed for docker containers.
[2024.6.21] - Changed choose_fastest_mirror.py to determine_fastest_mirror.py
[2024.6.20] - Added -m/--include_mrna to compile_metaeuk_identifiers.py for Issue #110
VERSION
file created indownload_databases.sh
--af_mode
with eitherrelaxed = max([Alignment_fraction_ref, Alignment_fraction_query]) > minimum_af
orstrict = (Alignment_fraction_ref > minimum_af) & (Alignment_fraction_query > minimum_af)
toedgelist_to_clusters.py
,global_clustering.py
,local_clustering.py
, andcluster.py
.pigz
toVEBA-annotate_env
which isn't a problem with mostconda
installations but needed fordocker
containers.choose_fastest_mirror.py
todetermine_fastest_mirror.py
-m/--include_mrna
tocompile_metaeuk_identifiers.py
for Issue #110