Installation

Table of Contents

• Linux
• Mac OSX
• Windows
• Vienna package

Linux

On most linux operating systems installations of Python should include the pip tool. If not use your distributions package manager to install pip first. Then the simple call below should install all dependencies. However if this fails see the linux section below for commands to run for installing any pre-requisites that might not be on your system. We hope to provide a snap package that will simplify installation on linux.

pip install smallrnaseq

For python 3 installs

You may need to use the command pip3 instead if python 2 is also on your system, like in Ubuntu. When installing packages with apt you likely need to specify python 3. e.g. python3-numpy instead of python-numpy.

For python 2.7 ONLY

You might also need the future package. Run pip install future to install.

If pip fails you can run the following commands first to fix likely missing packages. These are mainly needed for HTSeq to install. Then run pip again.

Ubuntu

sudo apt install python-dev samtools BEDtools liblzma-dev libbz2-dev zlib1g-dev python-scipy zlib1g-dev liblzo2-dev
sudo pip install smallrnaseq
sudo apt install bowtie

Fedora

sudo dnf install zlib-devel bzip2-devel xz-devel samtools swig redhat-rpm-config python-devel
sudo pip install cython pysam
sudo pip install smallrnaseq
sudo dnf install bowtie

Mac OSX

You will need to make sure you have Python. Anaconda is recommended as it provides most of the package requirements built in. Follow these steps in order:

• Download and run the Mac OS X installer from https://www.continuum.io/downloads. The installer will automatically configure your system to use the Anaconda Python. Close the terminal and start a new one.
• You should then add the bioconda channels:

conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda

• Type this command to install the remaining requirements: conda install pybedtools bx-python HTseq
• smallrnaseq can then be installed using pip: pip install smallrnaseq

bowtie on OSX:

You can install bowtie with conda too but it may hang or give an error on the latest version of OSX (Sierra). Running conda install bowtie=1.1.2 will install the older version which should work.

Windows

In theory this package will work on Windows but has not been tested. If you are a windows user it is recommended to use linux running inside virtualbox. See http://www.makeuseof.com/tag/how-to-use-virtualbox/

Vienna package

This is needed if you want to do novel miRNA prediction. It has to be installed separately on all systems. Go to https://www.tbi.univie.ac.at/RNA/#binary_packages and download the binary for your system.

Required dependencies

• numpy
• pandas
• matplotlib
• seaborn (requires scipy)
• HTSeq
• scikit-learn