User Tools

Site Tools


ray-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
ray-software [2014/09/01 14:21]
aorth [Installation]
ray-software [2015/06/09 16:37] (current)
aorth
Line 6: Line 6:
   * Version: 2.3.1   * Version: 2.3.1
   * Added: August, 2014   * 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/   * Link: http://denovoassembler.sourceforge.net/
  
 ===== Usage ===== ===== 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 ====== ===== Installation ======
 Notes from the sysadmin during 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 HAVE_LIBZ=y HAVE_LIBBZ2=y +make PREFIX=/export/apps/ray/2.3.1 HAVE_LIBZ=y HAVE_LIBBZ2=y 
-strip Ray +strip Ray 
-sudo mkdir -p /export/apps/ray/2.3.1 +sudo mkdir -p /export/apps/ray/2.3.1 
-sudo chown -R aorth:aorth /export/apps/ray/2.3.1 +sudo chown -R aorth:aorth /export/apps/ray/2.3.1 
-make install +make install 
-sudo chown -R root:root /export/apps/ray/2.3.1</code>+sudo chown -R root:root /export/apps/ray/2.3.1</code>
ray-software.1409581272.txt.gz · Last modified: 2014/09/01 14:21 by aorth