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--- trinity-software [2015/02/12 11:41] – [Information] aorth
+++ trinity-software [2015/03/20 15:32] – [Usage] aorth
@@ Line 13: / Line 13: @@
 <code>module avail trinity</code>
+**Note:** Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to ///var/scratch// instead of your home folder. For example:
+<code>#!/bin/env bash
+#SBATCH -p highmem
+#SBATCH -J trinity
+#SBATCH -n 10
+module load trinity/v2.0.3
+module load bowtie/1.1.1
+module load samtools/1.2
+# cd to working dir just in case
+export WORKDIR=$SLURM_JOBID
+cd $WORKDIR
+# match CPUs to amount requested in SBATCH options!
+Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 10 --output trinity-fish2</code>
 ===== Installation ======
 Notes from the sysadmin during installation: