NASExperiments/setup.sh at main · sayangoswami/NASExperiments · GitHub

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#!/bin/bash

export EXPDIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
cd $EXPDIR

# Create directory structure
mkdir code log out results tmp

# setup minimap2
cd $EXPDIR/code
git clone https://github.com/lh3/minimap2.git
cd minimap2
make -j8

# setup collinearity
cd $EXPDIR/code
git clone --recursive https://github.com/ratschlab/collinearity.git
cd collinearity

# for python bindings
pip install .

# to build from source
mkdir build && cd build
cmake ..
make -j 8

# setup metagraph
cd $EXPDIR/code
git clone --recursive https://github.com/ratschlab/metagraph.git
cd metagraph

# install sdsl lite
git submodule sync
git submodule update --init --recursive

pushd metagraph/external-libraries/sdsl-lite
./install.sh $PWD
popd

mkdir metagraph/build
cd metagraph/build

cmake ..
make -j 8

# setup spumoni
cd $EXPDIR/code
git clone --recursive https://github.com/ratschlab/spumoni.git
cd spumoni
mkdir build && cd build
cmake ..
make -j 16
make install

# python bindings
cd ..
pip install .

# setup rawhash
cd $EXPDIR/code
git clone -b cmake_merge --recursive https://github.com/ratschlab/RawHash.git rawhash2
cd rawhash2
git submodule update --init --recursive
mkdir -p build && cd build
cmake NOHDF5=1 NOPOD5=1 ..
make -j 8

# for python bindings
cd ..
pip install .

# Setup Minknow API Simulator
cd $EXPDIR/code
git clone https://github.com/ratschlab/MinknoApiSimulator.git
cd MinknoApiSimulator/certs
./generate.sh
cd ..
pip install .

cd $EXPDIR