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--- ray-software [2014/08/28 12:11] – [Usage] aorth
+++ ray-software [2015/06/09 16:37] (current) – 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/
 ===== Usage =====
-=== See versions of ray which are available ===
+See versions of ray which are available:
-<code>module avail ray</code>
+<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 ${OUTDIR}</code>
+Save in a file and submit using ''sbatch ray-mpi.sbatch''.
-=== See the built-in help ===
-<code>Ray -help | less</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>cd /tmp
+<code>$ cd /tmp
-git clone https://github.com/sebhtml/RayPlatform.git
+$ git clone https://github.com/sebhtml/RayPlatform.git
-git clone https://github.com/sebhtml/ray.git
+$ git clone https://github.com/sebhtml/ray.git
-cd ray
+$ cd ray
-git checkout v2.3.1
+$ git checkout v2.3.1
-scl enable devtoolset-1.1 bash
+$ scl enable devtoolset-1.1 bash
-module load openmpi/1.8.2
+$ 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
-sudo mkdir -p /export/apps/ray/2.3.1
+$ strip Ray
-sudo chown -R aorth:aorth /export/apps/ray/2.3.1
+$ sudo mkdir -p /export/apps/ray/2.3.1
-make install
+$ sudo chown -R aorth:aorth /export/apps/ray/2.3.1
-sudo chown -R root:root /export/apps/ray/2.3.1</code>
+$ make install
+$ sudo chown -R root:root /export/apps/ray/2.3.1</code>