add kraken2 special rule into TPV

templates/galaxy/config/tpv_rules_meta.yml.j2

@@ -62,6 +62,57 @@ tools:
         cores: int(job.get_param_values(app)['__job_resource']['cores'])
         context:
            walltime: "{int(job.get_param_values(app)['__job_resource']['time'])}"
+# DEMON: Hopefully, this could be optimized after TPV will get repeated reevaluation of resources (https://github.com/galaxyproject/total-perspective-vortex/issues/189)
+  toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/.*:
+    rules:
+      - id: set_highmem_based_on_ref_size
+        if: |
+          import os
+          import functools
+          from typing import Optional
+
+          @functools.lru_cache(maxsize=128)
+          def get_ref_size(lookup_value: str, table_name: str, lookup_column: str, value_column: str, value_template: str) -> Optional[int]:
+              ref_size = None  # optional int will be None unless set
+              try:
+                  table_value = app.tool_data_tables.get(table_name).get_entry(
+                      lookup_column, lookup_value, value_column
+                  )
+                  if table_value is not None:
+                      table_value = value_template.format(value=table_value)
+                      ref_size = int(os.path.getsize(table_value) / 1024**3)
+                      log.debug(
+                          "Data table '%s' lookup '%s=%s: %s=%s': %s GB",
+                          table_name, lookup_column, lookup_value,
+                          value_column, table_value, ref_size
+                      )
+                  else:
+                      log.warning(
+                          "Data table '%s' lookup '%s=%s: %s=None' returned None!, defaulting to %s",
+                          table_name, lookup_column, lookup_value,
+                          value_column, ref_size
+                      )
+              except OSError:
+                  log.exception("Failed to get size of: %s", table_value)
+              return ref_size
+
+          default_mem = 64
+          options = job.get_param_values(app)
+          lookup_value = options["kraken2_database"]
+
+          ref_size = get_ref_size(
+            lookup_value=lookup_value,
+            table_name="kraken2_databases",
+            lookup_column="value",
+            value_column="path",
+            value_template="{value}/hash.k2d",
+          )
+          ref_size is not None and min(ref_size * 1.2 + 48, 980) > 180
+        context:
+          queue: elixircz
+        scheduling:
+          require:
+            - highmem
   toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/.*:
     context:
       walltime: 48