add taskfarmer

kbase · Mar 13, 2024 · 3c0a818 · 3c0a818
1 parent fdb3dbd
commit 3c0a818
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/loaders/jobs/taskfarmer/task_generator.py b/src/loaders/jobs/taskfarmer/task_generator.py
@@ -49,10 +49,11 @@
 256 cores.
 '''
 
-TOOLS_AVAILABLE = ['gtdb_tk', 'checkm2', 'microtrait', 'mash']
+TOOLS_AVAILABLE = ['gtdb_tk', 'checkm2', 'microtrait', 'mash', 'eggnog']
 
 # estimated execution time (in minutes) for each tool to process a chunk of data
 TASK_META = {'gtdb_tk': {'chunk_size': 1000, 'exe_time': 65},
+             'eggnog': {'chunk_size': 500, 'exe_time': 65},  # TODO: update this value after performance testing
              'default': {'chunk_size': 5000, 'exe_time': 60}}
 NODE_TIME_LIMIT = 5  # hours  # TODO: automatically calculate this based on tool execution time and NODE_THREADS
 MAX_NODE_NUM = 100  # maximum number of nodes to use