SPAdes

Introduction

Pavel Pevzsner's de-novo assembler, primarily for - but not restricted to - bacteria.

Installation (Sysadmin notes)

Initially version 3.7.0 was insatlled 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. Therefore it's pretty to create a quick compile script which actually only needs two lines:

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. There is however, this:

<spades installation dir>/spades.py --test