SPAdes
Introduction
Pavel Pevszner's de-novo assembler, primarily for - but not restricted to - bacteria.
Usage
Example qsub job script
#!/bin/bash
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -V
#$ -q unstable.q
#$ -pe multi 16
# some quick "argument accounting"
EXPECTED_ARGS=1 # change value to suit!
if [ $# -ne $EXPECTED_ARGS ]; then
echo "error, this script should be fed with one argument: a filelist of fastq(.gz) files"
exit
fi
module load SPAdes
N=( $(cat $1) )
NSZ=${#N[@]}
for((i=2; i<NSZ; i+=2)); do
R1=${N[$i]}
R2=${N[$(($i+1))]}
ON=${N[$i]%%_*}
# echo "spades.py -t 6 -o $ON --pe1-1 $R1 --pe1-2 $R2"
spades.py -t $NSLOTS -o $ON --pe1-1 $R1 --pe1-2 $R2
done
Installation (Sysadmin notes)
Initially version 3.7.0 was installed using the specially compiled gcc/4.9.3 compiler (available as a module). However the -b version of the module now uses Redhats devtoolset-2, so that this compiler is not necessary.
Boost however, is necessary. The cluster has the latest version: 1.60. Possibly compiled (well, the bits that can be compiled) with g++ 4.4.7. In any case, the location of boost is a problem, although the boost module on the cluster does create some useful environmental variables, the given stacks_compile script does recognise them.
In any case, the configure system is cmake, so a "build" subdirectory should be created. Inside that, a short compile script containined something the following should be created:
module load boost
cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=.. -DBoost_NO_BOOST_CMAKE=TRUE -DBoost_NO_SYSTEM_PATHS=TRUE -DBOOST_ROOT:PATHNAME=${BOOST_ROOT} -DBoost_INCLUDE_DIRS:FILEPATH=${BOOST_INCLUDEDIR} -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_LIBRARYDIR} ../src
There is no make test nor make check. What there is, however, is a test script in the installation (not the source) directory, whihc can be invoked as follows:
<spades installation dir>/spades.py --test
or
<spades installation dir>/truspades.py --test
For the truspades modality.
