News Brief

24/10/2012 - Wolfpack Cluster's launched! Check out the User Guide now!

Galaxy Tools Benchmarks

Tool Name Dataset 4 8 16 32 64 Cores to assign?
bwa illumina dataset_6874.dat 44:38.00 28:37.07 21:36.46 18:19.18 19:12.39 8
40:39.20 27:03.90 20:49.99 18:05.82 20:11.93
bowtie illumina dataset_7422, dataset_7423 2:26:38.17 1:17:28.28 43:04.47 28:07.83 35:34.05 16
dataset_7530_dat, dataset_7531_dat 2:18:40.81 1:13:06.11 41:21.22 25:04.76 33:07.11
bowtie2 dataset_7530_dat, dataset_7531_dat 3:29:34.74 2:23:13.38 2:03:24.10 2:47:00.28 > 2:50:00 8
dataset_7539_dat 1:01:21.65 32:50.73 20:56.23 48:23.89 1:19:23.49
bowtie2 2.0.0-beta7 dataset_7539_dat 56:45.56 39:55.73 36:57.86 55:56.09
dataset_7539_dat 2:22:40.73 59:35.33 44:52.41 38:58.08 55:24.78
tophat illumina dataset_6146.dat 2:00:55.88 1:55:22.28 1:56:51.20 2:00:29.05 2:04:51.09
dataset_7539_dat 9:41:08.53 6:51:03.93 5:06:14.61 4:35:09.03 5:04:35.19 8
tophat2 v2.0.5 dataset_7539_dat 17:37:36.25 12:35:45.78 13:32:11.21 17:29:02.70 23:31:34.84 8
cufflinks dataset_6170.dat 32:20.57 22:59.54 18:08.41 15:34.00 14:50.94 16
cuffdiff dataset_6498.dat,dataset_6156.dat,dataset_6151.dat 2:04:27.59 1:16:37.78 1:00:22.27 54:36.90 51:18.34 16
cuffmerge dataset_5595.dat,dataset_5537.dat,dataset_5541.dat,dataset_5545.dat 17:14.33 9:20.87 5:30.10 3:36.31 2:34.21 16
groomer parallel dataset_5349_dat (15G) 2:46:16.87 1:27:55.15 48:07.74 28:08.39 12:28.92 16
dataset_6743 (47G) 1 core: 2831.13 min 798.523506016667 min 430.29483505 min 248.6161081 min 121.2450673333 72.434825716667
dataset_6743 (47G) 1 core: 47:04:01.08 11:59:42.26 6:27:40.92 3:33:12.71 2:06:53.40 1:00:23.02
GATK 4 (default)
ABySS 1.3.4 Two Seagrass FASTQ converted to FASTA (30GB each) Sinle-Core: ~60 Hrs SMP, 8-Core: ~17.6 Hrs SMP, 16-Core: ~13-16 Hrs SMP, 32-Core: ~17 Hrs SMP, 64-Core: ~24 Hrs MPI, 192-Core: ~30 Hrs

Galaxy Tools Dependencies Version

Tool Galaxy Main PWBC CBL Note
bowtie 0.12.7 0.12.7
bowtie2 Not Installed 2.0.0-beta5
BWA 0.5.6 0.5.9-r16
ClustalW 2.1 2.1
cufflinks 1.3.0 2.0.0 Downgrade is needed
cuffmerge 1.0.0 1.0.0
GATK 1.4 1.4
FastQC 0.10.0 0.10.0
Lastz 1.01.88 1.02.00
liftOver UCSC UCSC
macs 1.3 1.3.7.1
Blast+ (Megablast) 2.2.25 2.2.26
PerM 0.2.6 0.3.6
picardtools 1.76 1.68
samtools 0.1.18 0.1.18
tophat 1.4.0 1.4.1