Difference between revisions of "SPAdes"
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Pavel Pevszner's de-novo assembler, primarily for - but not restricted to - bacteria. | Pavel Pevszner's de-novo assembler, primarily for - but not restricted to - bacteria. | ||
| + | |||
| + | |||
| + | = Usage = | ||
| + | |||
= Installation (Sysadmin notes)= | = Installation (Sysadmin notes)= | ||
| − | Initially version 3.7.0 was | + | 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 Redhat''s devtoolset-2, |
so that this compiler is not necessary. | so that this compiler is not necessary. | ||
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For the truspades modality. | For the truspades modality. | ||
| + | |||
| + | = Links = | ||
| + | * [http://spades.bioinf.spbau.ru/release3.8.1/manual.html Official manual] | ||
Revision as of 12:44, 23 June 2016
Introduction
Pavel Pevszner's de-novo assembler, primarily for - but not restricted to - bacteria.
Usage
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.
