Packages to install

These command should work on the default StarCluster AMI, ami-999d49f0. These have already been pre-installed on the course AMI, ami-d6e581bf.

Install screed:

cd /usr/local/share
git clone https://github.com/ged-lab/screed.git
cd screed
python setup.py install

Install khmer:

cd /usr/local/share
git clone https://github.com/ged-lab/khmer.git
cd khmer
make

Install Trimmomatic:

cd /root
curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.27.zip
unzip Trimmomatic-0.27.zip
cp Trimmomatic-0.27/trimmomatic-0.27.jar /usr/local/bin

Install FastQC:

cd /usr/local/share
curl -O http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip
unzip fastqc_v0.10.1.zip
chmod +x FastQC/fastqc

Install libgtextutils:

cd /root
curl -O http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.1.tar.bz2
tar xjf libgtextutils-0.6.1.tar.bz2
cd libgtextutils-0.6.1/
./configure && make && make install

cd /root
curl -O http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.2.tar.bz2
tar xjf fastx_toolkit-0.0.13.2.tar.bz2
cd fastx_toolkit-0.0.13.2/
./configure && make && make install

Install the Velvet assembler:

cd /root
curl -O http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.08.tgz
tar xzf velvet_1.2.08.tgz
cd velvet
make MAXKMERLENGTH=51
cp velvet? /usr/local/bin

Install bowtie2:

cd /root
curl -L -O 'http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.1.0%2F&ts=1365392377&use_mirror=superb-dca3'
mv bowtie2-2.1.0-source.zip* bowtie2-2.1.0-source.zip
unzip bowtie2-2.1.0-source
cd bowtie2-2.1.0
make
cp bowtie2* /usr/local/bin

Installing samtools:

cd /root
git clone git://github.com/samtools/samtools.git
make
cp samtools /usr/local/bin
cd misc
cp *.pl maq2sam-long maq2sam-short md5fa md5sum-lite wgsim /usr/local/bin/
cd ../bcftools
cp *.pl bcftools /usr/local/bin/

Install bowtie:

curl -O -L http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-x86_64.zip
unzip bowtie-0.12.7-linux-x86_64.zip
cp bowtie-0.12.7/bowtie* /usr/local/bin

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