Skip to content

Compiling Celera Assembler

Celera Assembler, also known as Whole-Genome Shotgun (WGS) Assembler, is a de novo whole-genome shotgun (WGS) DNA sequence assembler.[1]

Installed Version♯

Celera Assembler 8.3rc2 is installed on Proteus. Use the modulefile:

wgs/8.3rc2

You will need to load the modulefile python/2.7-current as a pre-requisite.

Download♯

Download from: http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/

This article describes building wgs-8.3rc2

Prerequisites♯

  • Python 2.x - use "module load python/2.7-current"

Build♯

kmer♯

First, cd into the directory wgs-8.3rc2/kmer. Edit the file Make.compilers to look like:

# -*- makefile -*-
#  Linux64, optimized
CC                := gcc
SHLIB_FLAGS       := -shared
CFLAGS_COMPILE    := -m64 -fPIC -D_REENTRANT -O3 -march=corei7-avx -mfpmath=sse -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
CLDFLAGS          :=
CLIBS             := -pthread -ldl
CXX               := g++
CXXFLAGS_COMPILE  := -m64 -fPIC -D_REENTRANT -O3 -march=corei7-avx -mfpmath=sse -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
CXXLDFLAGS        :=
CXXLIBS           := -pthread -ldl
ARFLAGS           := ruvs
INSTALL/          := Linux-amd64/
PERL              := /usr/bin/perl
.EXE              :=
.SO               := .so
.A                := .a
.O                := .o
CLD               := ${CC}
CXXLD             := ${CXX}
CCDEP             := ${CC} -MM -MG
CXXDEP            := ${CXX} -MM -MG
CLIBS             += -lm -lbz2
CXXLIBS           += -lm -lbz2
PYTHON            := ${PYTHONDIR}/bin/python
PYTHON_H          := ${PYTHONDIR}/include/python2.7/Python.h
CFLAGS_PYTHON     := -I${PYTHONDIR}/include/python2.7
WITHOUT           :=

Then:

[juser@proteusi01 kmer]$ make install

This creates the directory wgs-8.3rc2/kmer/Linux-amd64/ and installs executables, libraries, and include files into subdirectories there.

wgs-assembler♯

Next, cd into wgs-8.3rc2/src Edit the file c_make.as to add this line:

ARCH_CFLAGS=-O3 -march=corei7-avx -mfpmath=sse

Then, build:

[juser@proteusi01 src]$ make

This installs wgs-assembler etc. into wgs-8.3rc2/Linux-amd64/

Set Up to Use♯

Add these directories to the path:

${PREFIX}/wgs-8.3rc2/Linux-amd64/bin ${PREFIX}/wgs-8.3rc2/kmer/Linux-amd64/bin

References♯

[1] Celera Assembler official wiki