Merge pull request #1139 from usegalaxy-eu/bgruening-patch-8

add a few more rules from ORG, we should move this all to shared

files/galaxy/tpv/tools.yml

@@ -782,7 +782,8 @@ tools:
       singularity_enabled: true
 
   toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/.*:
-    cores: 8
+    cores: 24
+    mem: 250
     scheduling:
       prefer:
         - condor-tpv
@@ -793,17 +794,21 @@ tools:
         # see usegalaxy-eu/issues#473: https://github.com/usegalaxy-eu/issues/issues/473
         env:
           _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
+
+      - if: input_size < 0.1
+        cores: 1
+        mem: 4
       - if: 0.1 <= input_size < 1
+        cores: 12
+        mem: 92
+      - if: 1 <= input_size < 4
+        cores: 16
+        mem: 128
+      - if: 4 <= input_size < 8
         cores: 20
-        mem: 100
-      - if: 1 <= input_size < 2
-        cores: 30
-        mem: 200
-      - if: 2 <= input_size < 30
-        cores: 60
-        mem: 950
-      - if: input_size >= 30
-        fail:
+        mem: 190
+      - if: input_size >= 80
+        fail: |
           Too much data, we cannot support such large Trinity assemblies with our
           backend. Please use another server for your job.
 
@@ -1012,16 +1017,24 @@ tools:
     env:
       _JAVA_OPTIONS: -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
 
-  ## bag things 40 is enough for most of the jobs, a better rule is needed
   toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/.*:
-    cores: 16
-    mem: 40
+    cores: 24
+    mem: 80
     env:
       TERM: vt100
       _JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
     scheduling:
       accept:
         - pulsar
+    rules:
+      - id: unicycler_small_input_rule
+        if: input_size < 0.05
+        cores: 1
+        mem: 3.8
+      - id: unicycler_medium_input_rule
+        if: 0.05 <= input_size < 2
+        cores: 8
+        mem: 28
 
   toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/.*:
     scheduling:
@@ -1171,6 +1184,35 @@ tools:
       require:
         - singularity
 
+  toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/.*:
+    cores: 32
+    mem: 244
+    rules:
+      - id: bwa_mem2_small_input_rule
+        if: input_size < 0.25
+        cores: 2
+        mem: 7.6
+      - id: bwa_mem2_medium_input_rule
+        if: 0.25 <= input_size < 16
+        cores: 8
+        mem: 28
+      - id: bwa_mem2_large_input_rule
+        if: 16 <= input_size < 32
+        cores: 16
+        mem: 58
+      - id: bwa_mem2_xlarge_input_rule
+        if: 32 <= input_size < 64
+        cores: 24
+        mem: 120
+      - id: bwa_mem2_history_reference_rule
+        if: |
+          helpers.job_args_match(job, app, {"reference_source": {"reference_source_selector": "history"}})
+        # per https://github.com/bwa-mem2/bwa-mem2/issues/41 it's 28 * reference
+        mem: |
+          options = job.get_param_values(app)
+          size = options["reference_source"]["ref_file"].get_size()
+          min(max(float(size/1024**3) * 28, (input_size - float(size/1024**3)) * 2, 7.6), 120)
+
   toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*:
     cores: 20
     mem: min(max(input_size*1.2, 3.8), 256)