MirMark Installation Process

Copyright 2014, Lana Garmire, lgarmire@cc.hawaii.edu

By copying and running this code on your platform, you agree to the open source license agreement GPL v3. If you already are running Ubuntu, you can proceed to the Ubuntu installation instructions. If you want to run a platform independent image of the code, you may proceed to the Docker installation instructions.

Ubuntu Standalone Installation

Install Ubuntu.

Prepare Ubuntu

Execute the following (note if you have already installed MirMark, you will need to remove all files in /tmp that you downloaded otherwise wget will not copy the new files):

sudo apt-get update
sudo apt-get -y install python-software-properties software-properties-common
sudo add-apt-repository ppa:j-4/vienna-rna
sudo apt-get update
sudo apt-get -y install gbrowse 
sudo apt-get -y install default-jdk 
sudo apt-get -y install vienna-rna wget

# Make sure weka.jar is in your jvm location (replace default-java with your current version)
cd /tmp && wget http://mn.eng.hawaii.edu/~garmire/weka.jar && sudo cp weka.jar /usr/lib/jvm/default-java/jre/lib/ext/.

sudo apt-get -y install build-essential
cd /tmp && wget http://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz && tar zxvf miRanda-aug2010.tar.gz && cd miRanda-3.3a && ./configure && make && sudo make install

sudo apt-get -y install r-base r-base-dev

cd /tmp && wget http://mn.eng.hawaii.edu/~garmire/MirMarkRNApl.tgz && tar zxvf MirMarkRNApl.tgz && sudo cp MirMarkRNApl/*.pl /usr/share/perl5
cd /tmp && wget http://mn.eng.hawaii.edu/~garmire/MirMark.tgz && tar zxvf MirMark.tgz && sudo cp MirMark/*.* /usr/local/bin

Running MirMark Code

Run the test example by executing the code:

# Fetch the example files
cd ~
wget http://mn.eng.hawaii.edu/~garmire/MirMarkTest.tgz
tar zxvf MirMarkTest.tgz
cd MirMarkTest

# docker needs to connect the directory "MirMarkTest" to the Docker image
# It does this through the "-v {host directory:image directory}" option.
# The -w option establishes the working directory.
# All other mirmark perl scripts can be run in the same manner.

siteFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt site_features rf.site.model
# The result is stored in MirMarkTest/site_features.result
utrFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt utr_features rf.utr.model
# The result is stored in MirMarkTest/utr_features.result

Docker installation

Docker is another method of running code on a different OS like Windows or Mac. It works by running a virtual machine through VirtualBox. The list of commands below should work once Docker is installed.

First install Docker and make sure it is running.

Pull MirMark Image

The MirMark image should already be configured through the following Dockerfile. You should be able to pull this image by running in Docker: [docker pull dgarmire/mirmark]. You should be able to build this image by running [mkdir mirmark && wget http://mn.eng.hawaii.edu/~garmire/HTML/MirMark/Dockerfile && docker build -t dgarmire/mirmark .].

Running MirMark Code

To run the site and utr feature analysis using the example files provided:

# Fetch the example files
cd ~
wget http://mn.eng.hawaii.edu/~garmire/MirMarkTest.tgz
tar zxvf MirMarkTest.tgz
cd MirMarkTest

# docker needs to connect the directory "MirMarkTest" to the Docker image
# It does this through the "-v {host directory:image directory}" option.
# The -w option establishes the working directory.
# All other mirmark perl scripts can be run in the same manner.

docker run -w /tmp/mnt -v /home/docker/MirMarkTest:/tmp/mnt -t dgarmire/mirmark siteFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt site_features rf.site.model
# The result is stored in MirMarkTest/site_features.result
docker run -w /tmp/mnt -v /home/docker/MirMarkTest:/tmp/mnt -t dgarmire/mirmark utrFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt utr_features rf.utr.model
# The result is stored in MirMarkTest/utr_features.result