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NetProphet2 wiki

Welcome to NetProphet wiki! This wiki will help you setup and run NetProphet2 on your local machine (Mac or Linux), as well as on the HPC cluster. We use Miniconda to manage the environment and dependencies, for ease of isolation and development.

Installing on MacOS using Conda

1. Install Conda:
   Install miniconda3 (64bit) for Mac from https://conda.io.
   After installation, for MacOS Catalina:
   $ source ~/opt/miniconda3/bin/activate
$ conda init zsh
   For other MacOS versions:
   $ source ~/opt/miniconda3/bin/activate
$ conda init
   Restart the terminal.

   To verify installation, run: $ conda info
   You should see conda output its version, etc.

2. Add Conda channels:
   $ conda config --add channels bioconda
$ conda config --add channels conda-forge

3. Create NetProphet2 environment:
   $ conda create -n np2 r=3.2.1 readline=6.2 pcre snakemake=3.8.2 numpy=1.15 scipy
$ conda activate np2

4. Install brew & gawk:
   $ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
$ sudo chown -R $(whoami) /usr/local/share/man/man8
$ brew install gawk

5. Install dependencies:
   a. Install gfortran-6.1.pkg from: https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg
   b. Install FIRE library:
   $ cd $NETPROPHET2_DIR/SRC
$ unzip -q FIRE-1.1a.zip
$ cd FIRE-1.1a/
$ chmod 775 configure
$ ./configure
$ make
   c. Install MEME library:
   $ cd $NETPROPHET2_DIR/SRC/
$ mkdir -p meme/
$ tar zxf meme-5.1.0.tar.gz
$ cd meme-5.1.0
$ ./configure --prefix=${NETPROPHET2_DIR}/SRC/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt
$ make
$ make test
$ make install

6. Install custom R packages:
   $ cd $NETPROPHET2_DIR/SRC/R_pkgs
$ R
$ > install.packages("BayesTree_0.3-1.3.tar.gz")
$ > install.packages("lars_0.9-8.tar.gz”)
$ > q()
$> save workspace? Y

7. Setup Environment variables:
   Open ~/.bash_profile (for macOS Catalina, ~/.zsh_profile) and add the following:

NETPROPHET2_DIR=[your path to NetProphet_2.0 dir]
export NETPROPHET2_DIR

MEME_BIN=$NETPROPHET2_DIR/SRC/meme/bin
export MEME_BIN

MEME_LIB=$NETPROPHET2_DIR/SRC/meme/libexec/meme-5.1.0
export MEME_LIB

FIREDIR=$NETPROPHET2_DIR/SRC/FIRE-1.1a/
export FIREDIR

export PATH=$NETPROPHET2_DIR:$MEME_BIN:$MEME_LIB:$FIREDIR:$PATH

Save it.
Then execute $ source ~/.bash_profile (or ~/.zsh_profile on Catalina)

Start NetProphet: $ NetProphet2 -s -f config.json