<commit_before>#! /bin/bash
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get -q -y update
sudo apt-get -y install python-nova build-essential python-pip rabbitmq-server git mongodb cmake zlib1g-dev mpich2 samtools openjdk-7-jre subversion python-matplotlib unzip r-base unp cpanminus picard-tools gcc-4.7 g++-4.7 graphviz csh pkg-config sparsehash libboost-all-dev gawk
#gawk is for masurca 

sudo pip install pika
sudo pip install python-daemon
sudo pip install pymongo
sudo pip install requests
sudo pip install yapsy
sudo pip install numpy
sudo pip install biopython
#sudo pip install --upgrade python-novaclient

# Install Velvet
pushd /tmp/
sudo git clone git://github.com/dzerbino/velvet.git
cd velvet
sudo make 'CATEGORIES=9' 'MAXKMERLENGTH=99' 'LONGSEQUENCES=1' 'OPENMP=1'
sudo cp velveth /usr/bin
sudo cp velvetg /usr/bin
cd ..

# Install Kiki
sudo git clone git://github.com/GeneAssembly/kiki.git
cd kiki
sudo mkdir bin
cd bin
sudo cmake ..
sudo make ki
sudo cp ki /usr/bin

# Install BWA
cd ../..
sudo git clone git://github.com/lh3/bwa.git bwa
cd bwa
sudo make
sudo cp bwa ../../bin/

# Install A5
cd ../..
mkdir a5
cd a5
wget http://ngopt.googlecode.com/files/ngopt_a5pipeline_linux-x64_20120518.tar.gz
tar -xvf ngopt*
cd ngopt*
cp -R bin/* ../../../bin/a5/
cd ../..
rm -rf a5/

# Install A6
mkdir a6
cd a6
git clone https://github.com/levinas/a5.git .
cd ..
mv a6 ../bin/

# Install IDBA toolkit
mkdir idba
cd idba
wget http://hku-idba.googlecode.com/files/idba-1.1.0.tar.gz
tar -xf idba*
cd idba*
./configure
make
cd bin
rm *.o
rm Make*
cd ..
cp -R bin/ ../../../bin/idba/
cd ../..
rm -rf idba

#Install QUAST
mkdir ../bin/quast
wget https://downloads.sourceforge.net/project/quast/quast-2.1.tar.gz
tar -xf quast-2.1.tar.gz
cd quast-2.1/
cp -R * ../../bin/quast
cd ..

#Install SolexaQA
mkdir solexa
mkdir ../bin/solexa
cd solexa
wget http://sourceforge.net/projects/solexaqa/files/src/SolexaQA_v.2.1.zip
unzip SolexaQA_v.2.1.zip
cd SolexaQA_v.2.1/
cp * ../../../bin/solexa
chmod +x ../../../bin/solexa/DynamicTrim.pl
chmod +x ../../../bin/solexa/LengthSort.pl
cd ../..
rm -rf solexa

#Install Spades
cd ../bin<commit_msg>use latest quast (v2.2)<commit_after>#! /bin/bash
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get -q -y update
sudo apt-get -y install python-nova build-essential python-pip rabbitmq-server git mongodb cmake zlib1g-dev mpich2 samtools openjdk-7-jre subversion python-matplotlib unzip r-base unp cpanminus picard-tools gcc-4.7 g++-4.7 graphviz csh pkg-config sparsehash libboost-all-dev gawk
#gawk is for masurca 

sudo pip install pika
sudo pip install python-daemon
sudo pip install pymongo
sudo pip install requests
sudo pip install yapsy
sudo pip install numpy
sudo pip install biopython
#sudo pip install --upgrade python-novaclient

# Install Velvet
pushd /tmp/
sudo git clone git://github.com/dzerbino/velvet.git
cd velvet
sudo make 'CATEGORIES=9' 'MAXKMERLENGTH=99' 'LONGSEQUENCES=1' 'OPENMP=1'
sudo cp velveth /usr/bin
sudo cp velvetg /usr/bin
cd ..

# Install Kiki
sudo git clone git://github.com/GeneAssembly/kiki.git
cd kiki
sudo mkdir bin
cd bin
sudo cmake ..
sudo make ki
sudo cp ki /usr/bin

# Install BWA
cd ../..
sudo git clone git://github.com/lh3/bwa.git bwa
cd bwa
sudo make
sudo cp bwa ../../bin/

# Install A5
cd ../..
mkdir a5
cd a5
wget http://ngopt.googlecode.com/files/ngopt_a5pipeline_linux-x64_20120518.tar.gz
tar -xvf ngopt*
cd ngopt*
cp -R bin/* ../../../bin/a5/
cd ../..
rm -rf a5/

# Install A6
mkdir a6
cd a6
git clone https://github.com/levinas/a5.git .
cd ..
mv a6 ../bin/

# Install IDBA toolkit
mkdir idba
cd idba
wget http://hku-idba.googlecode.com/files/idba-1.1.0.tar.gz
tar -xf idba*
cd idba*
./configure
make
cd bin
rm *.o
rm Make*
cd ..
cp -R bin/ ../../../bin/idba/
cd ../..
rm -rf idba

#Install QUAST
mkdir ../bin/quast
wget https://downloads.sourceforge.net/project/quast/quast-2.2.tar.gz
tar -xf quast-2.2.tar.gz
cd quast-2.2/
# wget https://downloads.sourceforge.net/project/quast/quast-2.1.tar.gz
# tar -xf quast-2.1.tar.gz
# cd quast-2.1/
cp -R * ../../bin/quast
cd ..

#Install SolexaQA
mkdir solexa
mkdir ../bin/solexa
cd solexa
wget http://sourceforge.net/projects/solexaqa/files/src/SolexaQA_v.2.1.zip
unzip SolexaQA_v.2.1.zip
cd SolexaQA_v.2.1/
cp * ../../../bin/solexa
chmod +x ../../../bin/solexa/DynamicTrim.pl
chmod +x ../../../bin/solexa/LengthSort.pl
cd ../..
rm -rf solexa

#Install Spades
cd ../bin
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