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--- ray-software [2014/08/28 11:45] – created aorth
+++ ray-software [2014/09/26 14:01] – aorth
@@ Line 6: / Line 6: @@
   * Version: 2.3.1
   * Added: August, 2014
-  * K-mer size: 32 (default at compile time)
+  * Max K-mer length: 32 (default at compile time)
+  * Default K-mer lenght: 21
   * Link: http://denovoassembler.sourceforge.net/
@@ Line 14: / Line 15: @@
 <code>module avail ray</code>
+=== See the built-in help ===
+<code>Ray -help | less</code>
+=== Example batch job ===
+Running Ray on two different nodes via MPI with a total of 15 CPUs:
+<code>#!/bin/env bash
+#SBATCH -p batch
+#SBATCH -n 15
+#SBATCH -J ray
+#SBATCH --nodes=2
+module load ray/2.3.1
+readonly DATADIR=~/data/bfusca
+readonly OUTDIR=~/data/bfusca/ray-sept26
+# mpirun gets the number of processors from SLURM
+mpirun Ray -k 27 -p ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR}</code>
+Save in a file and submit using ''sbatch ray-mpi.sbatch''.
 ===== Installation ======
 Notes from the sysadmin during installation:
@@ Line 24: / Line 46: @@
 scl enable devtoolset-1.1 bash
 module load openmpi/1.8.2
-make PREFIX=/export/apps/ray/2.3.1
+make PREFIX=/export/apps/ray/2.3.1 HAVE_LIBZ=y HAVE_LIBBZ2=y
+strip Ray
 sudo mkdir -p /export/apps/ray/2.3.1
 sudo chown -R aorth:aorth /export/apps/ray/2.3.1
 make install
 sudo chown -R root:root /export/apps/ray/2.3.1</code>