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Install Notes Specific to Harvard Workshop 2016

Software installed (and commands run) specific for the Harvard Workshop 2016.

ANVI'O (version 2.0.2)

Install instructions were followed from ANVI'O WEBSITE.

Dependencies:

  • Prodigal (installed already)
  • HMMER (installed already)
  • sqlite (installed already)
  • numpy (installed already)
  • GSL
wget ftp://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz
tar -xzvf gsl-latest.tar.gz
cd gsl-2.2.1
./configure && make && sudo make install
  • Cython
sudo pip install cython
  • hdf5
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.17/src/hdf5-1.8.17.tar.bz2 
tar -jxvf hdf5-1.8.17.tar.bz2
cd hdf5-1.8.17 
./configure && make && sudo make install

To install ANVI'O:

sudo pip install anvio

Install tested with

anvi-self-test

HyPhy (version 2.2.7)

Install instructions were followed from HyPhy Github and personal communication with Steven Weaver. Installed pthreads option for multiprocessing.

Commands run:

git clone https://github.com/veg/hyphy.git
cd hyphy
git checkout 2.2.7
cmake ./
make HYPHY
sudo make install

To launch:

HYPHYMP

HIV-TRACE

Install instructions were followed from HIV Trace Github and personal communications with Steven Weaver.

Dependencies:

  • tn93
wget https://github.com/veg/tn93/archive/v1.0.3.tar.gz
tar -xzvf v1.0.3.tar.gz
cd tn93-1.0.3
cmake [-DCMAKE_INSTALL_PREFIX=/install/path DEFAULT /usr/local/] ./
sudo make install
  • pip3
sudo apt install python3-pip
  • numpy
pip3 install numpy
  • biopython
pip3 install biopython

To install HIV-TRACE:

pip3 install https://github.com/veg/hivtrace/archive/0.2.0.tar.gz --process-dependency-links

Hyphy-vision

Install of a local version of Hyphy-vision in instances where there are internet issues. Install instructions from personal communication with Steven Weaver.

As genomics user, download:

git clone https://github.com/veg/hyphy-vision
cd hyphy-vision
git checkout gh-pages

To then launch the application (from within hyphy-vision):

python -m SimpleHTTPServer 8000

Jupyter Configuration for QIIME Workshop

Needed to set up the Jupyter configuration to allow the jupyter notebook to be viewed externally.

Whilst logged in as genomics, created the configuration file:

jupyter notebook --generate-config

Then edited the IP address lines to:

c.NotebookApp.ip='*'

GATB (version 1.171)

Install instructions were followed from the GATB Github

Dependencies:

sudo pip install mathstats
sudo pip install pysam==0.8.3
sudo pip install pyfasta

To install GATB:

wget http://gatb-pipeline.gforge.inria.fr/versions/bin/gatb-pipeline-1.171.tar.gz 
tar -xzvf gatb-pipeline-1.171.tar.gz

And then need to copy all of the directories and the binary to /usr/bin:

sudo cp gatb /usr/bin
sudo cp -r bloocoo/ /usr/bin
sudo cp -r BEEST/ /usr/bin
sudo cp -r tools/ /usr/bin
sudo cp -r minia/ /usr/bin

Finally whilst logged in as genomics:

su master
sudo pip install networkx

Updating tbl2asn (for PROKKA)

Downloaded latest version, unpackaged, renamed and moved to /usr/bin/.

wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
gunzip linux64.tbl2asn.gz
mv linux64.tbl2asn tbl2asn
sudo chmod +x tbl2asn
sudo mv tbl2asn /usr/bin/

SRA toolkit (version 2.8.0)

Downloaded binaries for latest version, unpackaged and copied to /usr/bin/.

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.0/sratoolkit.2.8.0-ubuntu64.tar.gz
tar -xzvf sratoolkit.2.8.0-ubuntu64.tar.gz
cd sratoolkit.2.8.0-ubuntu64
sudo cp bin/* /usr/bin/

PILON (version 1.2.0)

Downloaded latest jar file and copied to /usr/bin/.

wget https://github.com/broadinstitute/pilon/releases/download/v1.20/pilon-1.20.jar 
sudo cp pilon-1.20.jar /usr/bin

VCFannotator

Downloaded, unpackaged and moved executable and dependencies to /usr/bin/.

wget https://sourceforge.net/projects/vcfannotator/files/vcfannotator_r2013-10-13.tgz/download
tar -xzvf download
cd vcfannotator_r2013-10-13
sudo cp VCF_annotator.pl /usr/bin/
sudo cp -r PerlLib /usr/bin
sudo cp Util/* /usr/bin

Reducevcf (version 12)

Downloaded, unpackaged and moved jar files to /usr/bin.

wget http://www.genomeview.org/jenkins/reducevcf-nightly/reducevcf-12.zip
unzip reducevcf-12.zip
sudo mv ajt-2.10.jar /usr/bin/
sudo mv ark-43.jar /usr/bin/
sudo mv scala-library.jar /usr/bin/
sudo mv reducevcf.jar /usr/bin/