Enable HTTPS in the security group.
BWA aligner
Do:
cd /root
wget -O bwa-0.7.5.tar.bz2 http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.5a.tar.bz2/download
tar xvfj bwa-0.7.5.tar.bz2
cd bwa-0.7.5a
make
cp bwa /usr/local/bin
samtools
Do:
cd /root
curl -L http://sourceforge.net/projects/samtools/files/latest/download?source=files >samtools.tar.bz2
tar xjf samtools.tar.bz2
mv samtools-* samtools-latest
cd samtools-latest/
make
cp samtools bcftools/bcftools misc/* /usr/local/bin
FRCAlign
First:
apt-get -y install libbz2-dev libboost-dev libboost-iostreams-dev libboost-program-options-dev libboost-thread-dev
Do:
cd /root
git clone https://github.com/vezzi/FRC_align
cd FRC_align
cd src/samtools;
make
cd ..
cd ..
./configure
make install
REAPR
Do:
cd /root
curl -O ftp://ftp.sanger.ac.uk/pub4/resources/software/reapr/Reapr_1.0.16.tar.gz
tar xzf Reapr_1.0.16.tar.gz
cd Reapr_1.0.16
export PERL_MM_USE_DEFAULT=1
export PERL_EXTUTILS_AUTOINSTALL=--defaultdeps
export MAKEFLAGS='-j4'
perl -MCPAN -e 'install File::Spec::Link'
./install.sh
ln -s /root/Reapr_1.0.16/reapr /usr/local/bin/reapr
Python modules
Do:
pip install biopython
pip install pysam
Install R
Do:
apt-get install r-base
scaffoldgap2bed
do:
cd /usr/local/bin
curl -O https://raw.github.com/lexnederbragt/sequencetools/master/scaffoldgap2bed.py
chmod 770 scaffoldgap2bed.py
An IPython notebook
do:
cd /usr/local/notebooks
curl -O https://raw.github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/master/practicals/Plot_insertsizes.ipynb
Create a new volume based on snapshot snap-78cf1764 and attach it to your running instance via the Amazon EC2 management interface. When it is attached, remember the partition (e.g. sdf is xvdf) and mount like:
mkdir /data2
mount /dev/xvdf /data2
Use the following practicals from https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/tree/master/practicals
Evaluating assemblies with FRCbam
Assembly improvement using REAPR
Note that you’ll have to adjust file paths and we’re skipping a few things (e.g. SNP calling)
use scp:
do:
scp -i /path/to/keyfile.pem root@ec-xx-xx-xx-.compute-1.amazonaws.com:/path/to/data ./
For IGV, download:
—
To connect to the IPython Notebook interface, connect to
(ignore/accept the security warning) and use the password ‘beacon’.
Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.
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For an introduction to the documentation format please see the reST primer.