From 88601353c022e8c2482343b9f13fb946946ff28e Mon Sep 17 00:00:00 2001
From: cat-bro <cathjb@gmail.com>
Date: Thu, 17 Aug 2023 22:41:43 +1000
Subject: [PATCH] Add entries for some tools running out of memory with default
 settings on Galaxy Australia

---
 tools.yml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/tools.yml b/tools.yml
index 2dadf99..24c966b 100644
--- a/tools.yml
+++ b/tools.yml
@@ -272,6 +272,7 @@ tools:
     mem: 90
   toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/.*:
     cores: 8
+    mem: 40
   toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_sort_filter/rxdock_sort_filter/.*:
     mem: 90
   toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/.*:
@@ -547,6 +548,9 @@ tools:
     env:
       OMP_NUM_THREADS: '{cores}'
       OMP_THREAD_LIMIT: '{cores}'
+  toolshed.g2.bx.psu.edu/repos/dnbenso/masurca_simple/masurca_simple/.*:
+    cores: 8
+    mem: 31
   toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/.*:
@@ -566,6 +570,8 @@ tools:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/.*:
     mem: 12
+  toolshed.g2.bx.psu.edu/repos/ethevenot/profia/profia/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/.*:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*:
@@ -576,6 +582,8 @@ tools:
     mem: 250
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/.*:
     cores: 12
+  toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/.*:
     mem: 90
   toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_colocalization/cardinal_colocalization/.*:
@@ -1060,6 +1068,10 @@ tools:
     mem: 15.2
   toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/.*:
     cores: 4
+  toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/.*:
+    mem: 8
+  toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/barrnap/barrnap/.*:
     cores: 3
   toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*:
@@ -1153,6 +1165,8 @@ tools:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/.*:
     cores: 4
+  toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*:
     cores: 2
     mem: 8
@@ -1160,6 +1174,9 @@ tools:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/.*:
     mem: 50
+  toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/.*:
+    cores: 4
+    mem: 15
   toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/.*:
     cores: 12
     mem: 12
@@ -1368,6 +1385,9 @@ tools:
     mem: 16
     env:
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+  toolshed.g2.bx.psu.edu/repos/iuc/minia/minia/.*:
+    cores: 2
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/.*:
     mem: 32
   toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/.*:
@@ -2021,6 +2041,10 @@ tools:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/novoplasty/novoplasty/.*:
     mem: 40
+    rules:
+    - id: novoplasty_small_input_rule
+      if: input_size < 0.2
+      mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/ont_fast5_api_compress_fast5/ont_fast5_api_compress_fast5/.*:
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/.*:
@@ -2363,6 +2387,8 @@ tools:
     mem: 64
   toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/.*:
     mem: 10
+  toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/.*:
     mem: 32
   toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/.*: