Installation

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.

pip install smallrnaseq

Required dependencies

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

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.

Linux

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
sudo pip install smallrnaseq

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

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/

Mac OSX (not tested yet)

Miniconda is recommended. To use it download and run the Mac OS X installer from http://conda.pydata.org/miniconda.html. The installer will automatically configure your system to use the Anaconda Python. You can then use pip to install the package as above. Please