2019-12

Dependencies

Install Firefox (need the Firefox browser to be able to open plots from the command line):See https://www.mozilla.org/en-GB/firefox/new/

Install Conda (allows specific software versions to be set up in a discrete environment): 

# Linux
curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > Miniconda3.sh;
chmod +x Miniconda3.sh;
./Miniconda3.sh;
# Mac
curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > Miniconda3.sh;
chmod +x Miniconda3.sh;
./Miniconda3.sh;
# Then open a new terminal window before using conda

Install XQuartz (Mac only, need to run a version of X11 to be able to open plots from the command line):See https://www.xquartz.org

Install BlobToolKit dependencies (best to run these commands one at a time to make sure there are no errors before proceeding):

# create a Conda environment with all remaining dependencies
conda create -n btk_env -c conda-forge -y python=3.6 docopt pyyaml ujson tqdm nodejs=10 yq;
conda activate btk_env;
conda install -c bioconda -y pysam seqtk;
conda install -c conda-forge -y geckodriver selenium pyvirtualdisplay;
pip install fastjsonschema;

# fetch BlobToolKit code by cloning the repositories
mkdir -p ~/blobtoolkit;
cd ~/blobtoolkit;
git clone https://github.com/blobtoolkit/blobtools2;
git clone https://github.com/blobtoolkit/viewer;
git clone https://github.com/blobtoolkit/specification;
git clone https://github.com/blobtoolkit/insdc-pipeline;

# install the Viewer packages  (It’s safe to ignore warnings about vulnerabilities as you won’t be making the viewer publicly accessible)
cd viewer;
npm install;
cd ..;

# fetch the NCBI taxdump
mkdir -p taxdump;
cd taxdump;
curl -L ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz | tar xzf -;
cd ..;