g++

g++ >=4.3

Perl

Perl needs to be installed at /usr/bin/perl

SMALT

Download ​smalt-0.4.3 or ​other versions

choose the right version of SMALT. If your system is linux x86_64

cp smalt_x86_64 smalt

Samtools

Download ​samtools-0.1.8 or ​other versions

Follow INSTALL instruction.

PASSion

cd path_to_passion/PASSION/
chmod +x *
sh compile.sh

Set PATH environment variable

Set SMALT, Samtools and PASSion's path to PATH environment variable.

For linux users:

vim ~/.bashrc or vim ~/.cshrc
export PATH=$PATH:path_to_smalt/smalt: path_to_samtools/samtools: path_to_passion/PASSION
(example: export PATH=$PATH:~/smalt-0.4.3:~/PASSION:~/tools/samtools-0.1.8)

Finally, reload .bashrc

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