• Version: 3.1.1
• Added: September, 2014
• Link: http://bioinf.spbau.ru/spades

module avail spades

#!/bin/env bash
#SBATCH -p highmem
#SBATCH -n 6
#SBATCH -J spades

module load spades/3.1.1

readonly DATADIR=~/data/bfusca
readonly OUTDIR=/var/scratch/aorth-spades-oct8

# create output directory
mkdir -p ${OUTDIR}

# run spades with 6 CPUs on mammoth (because 10/16 are already allocated)
# run spades with 384 GB of RAM (default is 250, but it ran out of memory before)
spades.py -k 27 -1 ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz -2 ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR} -t 6 -m 384

echo
echo "Remember to check (and clean!) output directory on mammoth:"
echo
echo "  ${OUTDIR}"

Notes from the sysadmin during installation:

sudo yum install cmake28.x86_64
cd /tmp
wget http://spades.bioinf.spbau.ru/release3.1.1/SPAdes-3.1.1.tar.gz
cd SPAdes-3.1.1
sed -i 's/cmake/cmake28/' spades_compile.sh
scl enable devtoolset-1.1 bash
sudo mkdir -p /export/apps/spades/3.1.1
sudo chown aorth:aorth /export/apps/spades/3.1.1
PREFIX=/export/apps/spades/3.1.1 ./spades_compile.sh
sudo chown -R root:root /export/apps/spades/3.1.1

After loading the module, consult the built-in help:

spades.py --help