Check out and Compile

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This page describes how to check out the latest unreleased version of the Celera Assembler from the subversion repository.

1) Make a place to build the assembler. All further steps should start from within this directory.

% mkdir wgs
% cd wgs

2) Download the assembler from SVN.

% svn checkout svn://svn.code.sf.net/p/wgs-assembler/svn/trunk/src src

3) Download and install kmer.

% svn checkout svn://svn.code.sf.net/p/kmer/code/trunk kmer
% cd kmer
% gmake install
% cd ..

4) (deprecated as of August 2011) Optional, download, configure, compile and install the UMD Overlapper. UMD Overlapper is developed at the University of Maryland. For detailed usage and run instructions, visit http://www.genome.umd.edu/overlapper.htm or http://sourceforge.net/projects/umdoverlapper/.

% mkdir -p UMDOverlapper/Linux-amd64
% cd UMDOverlapper/Linux-amd64
% curl -o completeUMDDist.tar.gz \
  ftp://ftp.genome.umd.edu/pub/completeUMDDist.tar.gz
% gzip -dc completeUMDDist.tar.gz | tar -xf -
% perl Install.perl
% cd ../..

5) (deprecated as of August 2011) Optional, download, configure, compile and install Figaro. Figaro is developed at the University of Maryland. For detailed usage and run instructions, visit http://amos.sourceforge.net/Figaro/Figaro.html.

% curl -o Figaro.tar.gz \
  http://internap.dl.sourceforge.net/sourceforge/amos/Figaro-1.05.tar.gz
% gzip -dc Figaro.tar.gz | tar -xf -
% mkdir -p figaro
% mv Figaro-1.05 figaro/Linux-amd64
% cd figaro/Linux-amd64
% make install
% cd ../..

6) Compile and install the Celera Assembler. Binaries are installed into an architecture specific directory, for example, Linux-amd64. If UMD Overlapper or figaro are compiled, this step will also copy those modules to the architecture specific directory.

% cd src
% gmake

7) Check that several key executables exist. overmerry is built if kmer is correctly installed, runUMDOverlapper is built if the UMD overlapper is installed, figaro is built if figaro is installed. This directory can be moved to a system-wide location if desired.

% cd ..
% ls -l Linux-amd64/bin/gatekeeper
% ls -l Linux-amd64/bin/cgw
% ls -l Linux-amd64/bin/overmerry
% ls -l Linux-amd64/bin/runUMDOverlapper
% ls -l Linux-amd64/bin/figaro