From 8cf87fa507937e9762452110ec3e4fe011deb2eb Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 4 Nov 2024 17:07:58 -0500
Subject: [PATCH 1/5] Add `mem` for all tools with `cores` and rescale some
 memory based on usegalaxy.org usage

---
 tools.yml | 185 ++++++++++++++++++++++++++++--------------------------
 1 file changed, 96 insertions(+), 89 deletions(-)

diff --git a/tools.yml b/tools.yml
index 3a44773..38d360c 100644
--- a/tools.yml
+++ b/tools.yml
@@ -2,6 +2,7 @@ global:
   default_inherits: default
 tools:
   default:
+    abstract: true
     gpus: 0
     cores: 1
     mem: cores * 3.8
@@ -30,15 +31,17 @@ tools:
     cores: 1
     mem: 20
   toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/.*:
+    # noqa: T102
     cores: 4
   toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/.*:
     cores: 8
     mem: 92
   toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/.*:
     cores: 10
-    mem: 90
+    mem: 24
     env:
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
   toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/.*:
@@ -108,7 +111,7 @@ tools:
     mem: 24
   toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/.*:
     cores: 10
-    mem: 24
+    mem: 14
   toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/.*:
     cores: 10
     mem: 24
@@ -120,7 +123,7 @@ tools:
     mem: 24
   toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*:
     cores: 10
-    mem: 30
+    mem: 24
   toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/.*:
     cores: 10
     mem: 24
@@ -240,6 +243,7 @@ tools:
       mem: 80
   toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/.*:
     cores: 4
+    mem: 7
     env:
       CUDA_VISIBLE_DEVICES: 0
   toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/.*:
@@ -257,6 +261,7 @@ tools:
     cores: 5
     mem: 12
   toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_polya/nanopolish_polya/.*:
+    # noqa: T102
     cores: 3
   toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/.*:
     cores: 5
@@ -266,6 +271,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/bgruening/numeric_clustering/numeric_clustering/.*:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/bgruening/openduck_run_smd/openduck_run_smd/.*:
+    # noqa: T102
     gpus: 1
     cores: 1
     env:
@@ -298,10 +304,10 @@ tools:
   toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_sort_filter/rxdock_sort_filter/.*:
     mem: 90
   toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/.*:
-    cores: 6
-    mem: 70
+    cores: 8
+    mem: 48
   toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*:
-    cores: 6
+    cores: 8
     mem: 70
   toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_model_validation/sklearn_model_validation/.*:
     cores: 10
@@ -325,12 +331,15 @@ tools:
     mem: 24
   toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/.*:
     cores: 5
+    mem: 20
   toolshed.g2.bx.psu.edu/repos/bgruening/xchem_pose_scoring/xchem_pose_scoring/.*:
+    # noqa: T102
     gpus: 1
     cores: 1
     env:
       CUDA_VISIBLE_DEVICES: 0
   toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/.*:
+    # noqa: T102
     gpus: 1
     cores: 1
     env:
@@ -356,6 +365,7 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/.*:
     cores: 8
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/.*:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/.*:
@@ -390,7 +400,7 @@ tools:
       - docker
   toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/.*:
     cores: 8
-    mem: 20
+    mem: 12
     env:
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
     scheduling:
@@ -403,6 +413,7 @@ tools:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/.*:
     cores: 8
+    mem: 14
   toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/.*:
@@ -418,7 +429,7 @@ tools:
     mem: 10
   toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/.*:
     cores: 6
-    mem: 40
+    mem: 16
   toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/.*:
     cores: 6
     mem: 30
@@ -442,18 +453,19 @@ tools:
   toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/.*:
-    mem: 30.4
+    mem: 24
   toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/.*:
     mem: 30.4
   toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/.*:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/.*:
-    cores: 8
+    cores: min(max(int(input_size * 4), 1), 16)
+    mem: min(max(int(input_size * 7), 5.6), 64)
   toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/.*:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*:
     cores: 10
-    mem: 90
+    mem: 48
   toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/.*:
     mem: 34.2
   toolshed.g2.bx.psu.edu/repos/devteam/hisat/hisat/.*:
@@ -472,6 +484,7 @@ tools:
     mem: 40
   toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/.*:
     cores: 8
+    mem: 40
     rules:
     - id: pulsar_rule
       if: |
@@ -492,82 +505,15 @@ tools:
     mem: 40
   toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/.*:
     cores: 16
+    mem: 64
   toolshed.g2.bx.psu.edu/repos/devteam/picard/.*:
     cores: 3
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/.*:
-    mem: 12
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardGCBiasMetrics/.*:
-    mem: 12
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardHsMetrics/.*:
     mem: 12
     env:
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/.*:
-    mem: 12
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/.*:
-    mem: 12
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/.*:
-    mem: 12
-    env:
       TMP_DIR: $TMPDIR
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/.*:
-    mem: 12
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/.*:
-    mem: 12
   toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/.*:
     mem: 10
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/rgEstLibComp/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/.*:
-    mem: 12
-    env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
   toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/.*:
     mem: 32
     env:
@@ -579,6 +525,7 @@ tools:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/.*:
     cores: 5
+    mem: 24
   toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/.*:
@@ -588,8 +535,8 @@ tools:
     cores: 2
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/.*:
-    cores: 10
-    mem: 90
+    cores: 16
+    mem: 64
   toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/.*:
     mem: 32
     env:
@@ -639,10 +586,12 @@ tools:
     cores: 24
     mem: 200
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/dorado_pod5_convert/dorado_pod5_convert/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hapcut2/hapcut2/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/.*:
+    # noqa: T102
     cores: 12
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/.*:
     cores: 16
@@ -699,10 +648,13 @@ tools:
     mem: 92
   toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/.*:
     cores: 16
+    mem: 64
   toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant_mqpar/.*:
     cores: 16
+    mem: 64
   toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant_mqpar/maxquant_mqpar/.*:
     cores: 16
+    mem: 64
   toolshed.g2.bx.psu.edu/repos/galaxyp/metagene_annotator/metagene_annotator/.*:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/galaxyp/morpheus/morpheus/.*:
@@ -1107,13 +1059,16 @@ tools:
   toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_clip/je_clip/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/.*:
     cores: 8
     mem: 20
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
     cores: 16
@@ -1140,12 +1095,14 @@ tools:
     mem: 70
   toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/.*:
     cores: 4
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/.*:
     mem: 2 + input_size * 10
   toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/.*:
     mem: 15.2
   toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/.*:
     cores: 4
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/arriba/arriba/.*:
@@ -1159,6 +1116,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/.*:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/iuc/barrnap/barrnap/.*:
+    # noqa: T102
     cores: 3
   toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*:
     mem: 15
@@ -1166,8 +1124,10 @@ tools:
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
   toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/.*:
     cores: 7
+    mem: 20
   toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/.*:
     cores: 2
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/.*:
     mem: 40
   toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/.*:
@@ -1208,10 +1168,10 @@ tools:
     mem: 100
   toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/.*:
     cores: 10
-    mem: 80
+    mem: 24
   toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/.*:
     cores: 1
-    mem: 60
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/.*:
     cores: 1
     mem: 60
@@ -1250,6 +1210,7 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/.*:
     cores: 8
+    mem: 32
   toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/.*:
     mem: 25
   toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/.*:
@@ -1269,6 +1230,7 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/.*:
     cores: 30
+    mem: 24
   toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/.*:
@@ -1355,6 +1317,7 @@ tools:
     mem: 30.4
   toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/.*:
     cores: 4
+    mem: 8
     env:
       MKL_NUM_THREADS: '{cores}'
       NUMBA_NUM_THREADS: '{cores}'
@@ -1372,6 +1335,7 @@ tools:
     mem: 122.8
   toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/.*:
     cores: 16
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/.*:
     cores: 8
     mem: 20
@@ -1412,6 +1376,7 @@ tools:
     mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/hyphy_prime/hyphy_prime/.*:
     cores: 20
+    mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/.*:
     cores: 20
     mem: 10
@@ -1428,6 +1393,7 @@ tools:
     mem: 24
   toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/.*:
     cores: 10
+    mem: 7
   toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/.*:
     mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/.*:
@@ -1450,6 +1416,7 @@ tools:
     mem: 20
   toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/.*:
     cores: 3
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/.*:
     cores: 8
     mem: 8
@@ -1474,11 +1441,13 @@ tools:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/.*:
     cores: 4
+    mem: 16
   toolshed.g2.bx.psu.edu/repos/iuc/lumpy_prep/lumpy_prep/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/lumpy_sv/lumpy_sv/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/maaslin2/maaslin2/1.16.0.*:
+    # noqa: T102
     cores: 1
   toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/.*:
     mem: 12
@@ -1526,6 +1495,7 @@ tools:
     mem: 48
   toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/.*:
     cores: 16
+    mem: 58
   toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/.*:
     cores: 2
     mem: 7.6
@@ -1612,6 +1582,7 @@ tools:
       TERM: vt100
   toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/.*:
     cores: 7
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/mothur_chop_seqs/mothur_chop_seqs/.*:
     cores: 2
     mem: 20
@@ -2188,6 +2159,7 @@ tools:
     mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/.*:
     cores: 5
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/nanocompore_sampcomp/nanocompore_sampcomp/.*:
     cores: 9
     mem: 48
@@ -2204,6 +2176,7 @@ tools:
       if: input_size < 0.2
       mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/ont_fast5_api_compress_fast5/ont_fast5_api_compress_fast5/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/.*:
     cores: 8
@@ -2213,8 +2186,10 @@ tools:
     mem: 30.7
   toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/.*:
     cores: 8
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/.*:
     cores: 7
+    mem: 58
   toolshed.g2.bx.psu.edu/repos/iuc/pharokka/pharokka/.*:
     cores: 8
     mem: 31
@@ -2236,7 +2211,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/.*:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/.*:
-    mem: 40
+    mem: 20
   toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/.*:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/.*:
@@ -2269,6 +2244,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/.*:
     mem: 30.4
   toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/.*:
+    cores: 6
     mem: 24
   toolshed.g2.bx.psu.edu/repos/iuc/qualimap_rnaseq/qualimap_rnaseq/.*:
     mem: 12
@@ -2276,6 +2252,7 @@ tools:
     cores: 10
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/raven/raven/.*:
+    # noqa: T102
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/.*:
     cores: 16
@@ -2293,6 +2270,7 @@ tools:
     mem: 250
   toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/.*:
     cores: 24
+    mem: 24
   toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/.*:
     cores: 1
     mem: 12
@@ -2309,7 +2287,8 @@ tools:
     cores: 4
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/.*:
-    cores: 9
+    cores: 8
+    mem: 28
   toolshed.g2.bx.psu.edu/repos/iuc/schicexplorer_schicadjustmatrix/schicexplorer_schicadjustmatrix/.*:
     cores: 5
     mem: 64
@@ -2360,18 +2339,20 @@ tools:
     mem: 64
   toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/.*:
     cores: 4
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/.*:
     mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/shasta/shasta/.*:
     cores: 10
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*:
-    cores: 4
-    mem: 50
+    cores: 8
+    mem: 32
     env:
       SHOVILL_RAM: '{int(mem)}'
   toolshed.g2.bx.psu.edu/repos/iuc/slamdunk/slamdunk/.*:
     cores: 10
+    mem: 30
   toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/.*:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/.*:
@@ -2421,33 +2402,41 @@ tools:
     mem: 4
   toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/.*:
     cores: 8
+    mem: 28
   toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/.*:
     mem: 20
   toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/.*:
-    cores: 3
+    cores: 4
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_clonefilter/stacks2_clonefilter/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/.*:
+    # noqa: T102
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_denovomap/stacks2_denovomap/.*:
     cores: 4
     mem: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/.*:
+    # noqa: T102
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_kmerfilter/stacks2_kmerfilter/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_refmap/stacks2_refmap/.*:
+    # noqa: T102
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_shortreads/stacks2_shortreads/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/.*:
+    # noqa: T102
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/.*:
     cores: 8
     mem: 42
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_ustacks/stacks2_ustacks/.*:
+    # noqa: T102
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks_clonefilter/stacks_clonefilter/.*:
     mem: 8
@@ -2478,17 +2467,23 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/.*:
     cores: 8
+    mem: 38
   toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/.*:
     mem: 15
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_cluster/trycycler_cluster/.*:
+    # noqa: T102
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_consensus/trycycler_consensus/.*:
+    # noqa: T102
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_partition/trycycler_partition/.*:
+    # noqa: T102
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_reconcile_msa/trycycler_reconcile_msa/.*:
+    # noqa: T102
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_subsample/trycycler_subsample/.*:
+    # noqa: T102
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/ucsc_wigtobigwig/ucsc_wigtobigwig/.*:
     mem: 20
@@ -2500,7 +2495,7 @@ tools:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/.*:
     cores: 16
-    mem: 90
+    mem: 60
     env:
       TERM: vt100
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
@@ -2613,6 +2608,7 @@ tools:
     cores: 4
     mem: 32
   toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/.*:
+    # noqa: T102
     cores: 4
   toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/.*:
     mem: 16
@@ -2639,6 +2635,7 @@ tools:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/.*:
     cores: 8
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft_add/.*:
     mem: 12
   toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/.*:
@@ -2663,6 +2660,7 @@ tools:
     cores: 12
     mem: 16
   toolshed.g2.bx.psu.edu/repos/rnateam/rnalien/RNAlien/.*:
+    # noqa: T102
     cores: 10
   toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/.*:
     mem: 80
@@ -2675,6 +2673,7 @@ tools:
     mem: 26.6
   toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/.*:
     cores: 4
+    mem: 14
   toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/.*:
     mem: 60
   toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align/.*:
@@ -2682,6 +2681,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/.*:
     mem: 22.8
   .*bowtie2_index_builder_data_manager.*:
+    # noqa: T102
     cores: 16
   .*bwa_mem_index_builder_data_manager.*:
     cores: 12
@@ -2693,10 +2693,13 @@ tools:
     cores: 1
     mem: 64
   .*data_manager_cat.*:
+    # noqa: T102
     cores: 5
   .*data_manager_diamond_database_builder.*:
+    # noqa: T102
     cores: 5
   .*data_manager_eggnog_mapper_abspath.*:
+    # noqa: T102
     cores: 5
   .*data_manager_funannotate.*:
     cores: 1
@@ -2704,12 +2707,15 @@ tools:
   .*data_manager_gemini_download.*:
     mem: 20
   .*data_manager_humann2_database_downloader.*:
+    # noqa: T102
     cores: 5
   .*data_manager_humann2_download.*:
     mem: 25
   .*data_manager_humann_database_downloader.*:
+    # noqa: T102
     cores: 5
   .*data_manager_interproscan.*:
+    # noqa: T102
     cores: 5
   .*data_manager_metaphlan_download.*:
     cores: 12
@@ -2730,6 +2736,7 @@ tools:
     cores: 12
     mem: 92
   .*kraken2_build_database.*:
+    # noqa: T102
     cores: 16
   .*kraken_database_builder.*:
     mem: 200

From fb30e09a9353c924308154662c1185d6125f5807 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 4 Nov 2024 18:00:19 -0500
Subject: [PATCH 2/5] Replace noqas with FIXMEs

---
 tools.yml | 57 +++++++++++++++++++++++++++++--------------------------
 1 file changed, 30 insertions(+), 27 deletions(-)

diff --git a/tools.yml b/tools.yml
index 38d360c..05134f2 100644
--- a/tools.yml
+++ b/tools.yml
@@ -31,10 +31,10 @@ tools:
     cores: 1
     mem: 20
   toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 4
   toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/.*:
     cores: 8
@@ -261,7 +261,7 @@ tools:
     cores: 5
     mem: 12
   toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_polya/nanopolish_polya/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 3
   toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/.*:
     cores: 5
@@ -586,12 +586,12 @@ tools:
     cores: 24
     mem: 200
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/dorado_pod5_convert/dorado_pod5_convert/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hapcut2/hapcut2/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiadapterfilt/hifiadapterfilt/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 12
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/.*:
     cores: 16
@@ -1059,16 +1059,16 @@ tools:
   toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_clip/je_clip/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/.*:
     cores: 8
     mem: 20
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
     cores: 16
@@ -1088,6 +1088,9 @@ tools:
     mem: 12
     env:
       _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+  toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1:
+    cores: 3
+    mem: 3.7
   toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/.*:
     mem: 30.4
   toolshed.g2.bx.psu.edu/repos/iuc/abyss/abyss-pe/.*:
@@ -1116,7 +1119,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/.*:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/iuc/barrnap/barrnap/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 3
   toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*:
     mem: 15
@@ -1235,6 +1238,7 @@ tools:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/.*:
     cores: 4
+    mem: 
   toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/.*:
     mem: 30
     rules:
@@ -2176,7 +2180,7 @@ tools:
       if: input_size < 0.2
       mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/ont_fast5_api_compress_fast5/ont_fast5_api_compress_fast5/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/.*:
     cores: 8
@@ -2252,7 +2256,7 @@ tools:
     cores: 10
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/raven/raven/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/.*:
     cores: 16
@@ -2411,32 +2415,32 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_clonefilter/stacks2_clonefilter/.*:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_denovomap/stacks2_denovomap/.*:
     cores: 4
     mem: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_kmerfilter/stacks2_kmerfilter/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_refmap/stacks2_refmap/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 8
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_shortreads/stacks2_shortreads/.*:
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/.*:
     cores: 8
     mem: 42
   toolshed.g2.bx.psu.edu/repos/iuc/stacks2_ustacks/stacks2_ustacks/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/stacks_clonefilter/stacks_clonefilter/.*:
     mem: 8
@@ -2471,19 +2475,19 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/.*:
     mem: 15
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_cluster/trycycler_cluster/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_consensus/trycycler_consensus/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 16
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_partition/trycycler_partition/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_reconcile_msa/trycycler_reconcile_msa/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/trycycler_subsample/trycycler_subsample/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 9
   toolshed.g2.bx.psu.edu/repos/iuc/ucsc_wigtobigwig/ucsc_wigtobigwig/.*:
     mem: 20
@@ -2542,7 +2546,8 @@ tools:
   toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/.*:
     mem: 32
   toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/.*:
-    cores: 5
+    cores: 8
+    mem: 28
   toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/.*:
     mem: 32
   toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/.*:
@@ -2608,7 +2613,7 @@ tools:
     cores: 4
     mem: 32
   toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 4
   toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/.*:
     mem: 16
@@ -2660,7 +2665,7 @@ tools:
     cores: 12
     mem: 16
   toolshed.g2.bx.psu.edu/repos/rnateam/rnalien/RNAlien/.*:
-    # noqa: T102
+    # FIXME: needs mem
     cores: 10
   toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/.*:
     mem: 80
@@ -2756,8 +2761,6 @@ tools:
     mem: 36
   CONVERTER_bedgraph_to_bigwig:
     mem: 8
-  Extract genomic DNA 1:
-    cores: 3
   bfast_wrapper:
     cores: 10
     mem: 20

From e04983cbfee8c313efe2841f74b7d86220140499 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 5 Nov 2024 12:03:44 -0500
Subject: [PATCH 3/5] Improvements based on review from @mira-miracoli

---
 tools.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tools.yml b/tools.yml
index 05134f2..d237fcb 100644
--- a/tools.yml
+++ b/tools.yml
@@ -464,8 +464,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/.*:
     mem: 16
   toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*:
+    # see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers
     cores: 10
-    mem: 48
+    mem: 9 + input_size * 1
   toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/.*:
     mem: 34.2
   toolshed.g2.bx.psu.edu/repos/devteam/hisat/hisat/.*:
@@ -1172,9 +1173,6 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/.*:
     cores: 10
     mem: 24
-  toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/.*:
-    cores: 1
-    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/.*:
     cores: 1
     mem: 60
@@ -1238,7 +1236,7 @@ tools:
     mem: 11.4
   toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/.*:
     cores: 4
-    mem: 
+    mem: min(max(int(input_size * 6), 3.7), 58)
   toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/.*:
     mem: 30
     rules:
@@ -1404,6 +1402,7 @@ tools:
     mem: 30.4
   toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/.*:
     cores: 8
+    mem: 12
     scheduling:
       accept:
       - pulsar
@@ -2193,7 +2192,7 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/.*:
     cores: 7
-    mem: 58
+    mem: min(max(int(input_size * 8), 3.7), 28)
   toolshed.g2.bx.psu.edu/repos/iuc/pharokka/pharokka/.*:
     cores: 8
     mem: 31
@@ -2350,8 +2349,9 @@ tools:
     cores: 10
     mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/.*:
-    cores: 8
-    mem: 32
+    # this should mirror spades
+    cores: 20
+    mem: min(max(int(input_size * 32), 14), 240)
     env:
       SHOVILL_RAM: '{int(mem)}'
   toolshed.g2.bx.psu.edu/repos/iuc/slamdunk/slamdunk/.*:
@@ -2575,7 +2575,7 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/nml/spades/spades/.*:
     cores: 20
-    mem: 330
+    mem: min(max(int(input_size * 32), 14), 240)
   toolshed.g2.bx.psu.edu/repos/pavlo-lutsik/rnbeads/rnbeads/.*:
     mem: 20
   toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/.*:

From 51b6fdf8e3acb7c30e5043d99bc11cb89860ddca Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Fri, 8 Nov 2024 13:14:51 -0500
Subject: [PATCH 4/5] Increase iqtree mem from review by @cat-bro

---
 tools.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools.yml b/tools.yml
index d237fcb..0afa9a9 100644
--- a/tools.yml
+++ b/tools.yml
@@ -1395,7 +1395,7 @@ tools:
     mem: 24
   toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/.*:
     cores: 10
-    mem: 7
+    mem: 19
   toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/.*:
     mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/.*:

From 0cfae499d24b98e914a1fdcbe04dd3db42049aeb Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 20 Nov 2024 14:00:26 -0500
Subject: [PATCH 5/5] Decrease tophat resources

---
 tools.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools.yml b/tools.yml
index 0afa9a9..473d054 100644
--- a/tools.yml
+++ b/tools.yml
@@ -536,8 +536,8 @@ tools:
     cores: 2
     mem: 7.6
   toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/.*:
-    cores: 16
-    mem: 64
+    cores: 8
+    mem: 32
   toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/.*:
     mem: 32
     env: