An overview of the approach implemented in miRge can be found at https://baraslab.github.io/miRge/.
Please cite https://www.ncbi.nlm.nih.gov/pubmed/26571139 when using miRge in publications, thanks!
miRge may be cloned from this repository by the following command:
git clone https://github.com/BarasLab/miRge.git
All required libraries may be installed on a ubuntu variant with this command:
sudo apt-get update
sudo apt-get install libgd-graph-perl libhtml-table-perl python-setuptools python-dev unzip
pip install cutadapt>=1.8.1 or easy_install cutadapt>=1.8.1
OR if you lack root privs
pip install --user cutadapt>=1.8.1 or easy_install --user cutadapt>=1.8.1
Note: if you install it as a non-root user, you must ensure the install location is on your path, or specify the location of cutadapt with the --cutadapt argument. This is usually in ~/.local/bin/cutadapt, but may vary with your particular distribution. At this time, miRge has been tested with cutadapt versions 1.8.1 through 1.11. Future versions may break compatibility
This version may not be the latest, visit the official Bowtie website for the latest version
wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-linux-x86_64.zip/download
It may be saved as 'download' or 'bowtie-xxx', so run 'unzip download.zip' to extract it to a given location
From within the directory miRge is installed in, run:
wget http://atlas.pathology.jhu.edu/baras/miRge/miRge.seqLibs.tar.gz
tar -zxvf miRge.seqLibs.tar.gz