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.

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. There is however, this:

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

The Stacks installation itself then needs a further two modifications which will make it depend on a particular running mysql server. It does seem to be the case that only one mysql server can be used for one Stacks installation, by the nature of these two modifications. The files to be modified are:

• <stack_root_dir>/share/stacks/php/constants.php
• <stack_root_dir>/share/stacks/sql/mysql.cnf

The settings in these files referring to the mysql server should be modified appropriately.