.. highlight:: shell ============ Installation ============ .. |pipimage| image:: https://img.shields.io/pypi/v/rnalysis.svg :target: https://pypi.python.org/pypi/rnalysis Latest version: |pipimage| *RNAlysis* stand-alone app (most beginner-friendly) ----------------------------------------------------- A stand-alone version of *RNAlysis* is available for both Windows and MacOS. This version is the most beginner-friendly to install, since it requires the least amount of setup to make it work. How to install it ^^^^^^^^^^^^^^^^^ You can download the latest stand-alone of *RNAlysis* from the `GitHub Releases page `_ ('RNAlysis-X.Y.Z_windows.zip' for Windows, and 'RNAlysis-X.Y.Z_macos.zip' for MacOS). If you use the *RNAlysis* stand-alone app, the only other programs you will need to install are external programs that interface with *RNAlysis* - such as `R `_ (if you want to use *DESeq2*), and `kallisto `_. How to run it ^^^^^^^^^^^^^ First, unzip the .zip file you downloaded. **On Windows:** After unzipping, enter the unzipped directory and open the "RNAlysis.exe" file: .. image:: /installation_screenshots/01b01_open_windows.png :width: 600 :alt: Open *RNAlysis* stand-alone app on Windows - Open "RNAlysis.exe" If this is the first time you launch *RNAlysis*, the following messagebox will show up. To get past it, first click on "More info": .. image:: /installation_screenshots/01b02_open_windows.png :width: 600 :alt: Open *RNAlysis* stand-alone app on Windows - click on "More info" Next, click on the "Run anyway" button at the bottom-right corner: .. image:: /installation_screenshots/01b03_open_windows.png :width: 600 :alt: Open *RNAlysis* stand-alone app on Windows - click on "Run anyway" The *RNAlysis* app should launch now - this may take a minute or two, so be patient! **On MacOS:** After unzipping, open the "RNAlysis.dmg" file. The *RNAlysis* app should launch now - this may take a minute or two, so be patient! Further guidance ^^^^^^^^^^^^^^^^^ If you need further guidance with installing the stand-alone version of *RNAlysis*, please follow this `installation guide `_ which was kindly provided by `Prof. Matthias Wilm `_. Install as a Python package with *pip* (best performance) ---------------------------------------------------------- You can install *RNAlysis* as a Python package via `pip`_. How to install it ^^^^^^^^^^^^^^^^^ If you don't have `pip`_ installed, this `Python installation guide`_ can guide you through the process. To install the full version of *RNAlysis* (includes additional features that might not work out-of-the-box on all machines), you should first install `GraphViz `_, `R`_, and `kallisto`_. **On Windows:** you may also need to install `Microsoft Visual C++ 14.0 `_ or greater, and `Perl `_. **On Linux:** you may also need to install **Qt 5 Image Formats** to view tutorial videos from within *RNAlysis*. To do so on Debian/ubuntu systems, use the command `sudo apt install qt5-image-formats-plugins`. To do so on Red Hat-based distros such as Fedora, use the command `dnf install qt5-qtimageformats`. After installing these external dependencies, you can install *RNAlysis* by typing the following command in your terminal window:: pip install RNAlysis[all] If you're having trouble installing the full version of *RNAlysis*, you can install the basic version first. To install the basic version of *RNAlysis*, use the following command in your terminal window:: pip install RNAlysis You can also install *RNAlysis* with only some of the following additional features: * `fastq` - adapter trimming and RNA-seq transcript quantification of Fastq files * `hdbscan` - clustering analysis using the HDBSCAN method * `single-set` - single-set enrichment analysis using the XL-mHG test * `randomization` - improved performance for randomization tests * `reports` - automatically generate interactive analysis reports by calling the install command with one or more additional features inside the square brackets, separated by commas. For example:: pip install RNAlysis[fastq,single-set] will install the basic version of *RNAlysis*, along with the `fastq` and `single-set` additional features. .. _pip: https://pip.pypa.io .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ How to run it ^^^^^^^^^^^^^ If you installed *RNAlysis* with *pip*, you can open the *RNAlysis* app by executing the command `rnalysis-gui` from your terminal. Alternatively, you can open the *RNAlysis* app by typing the following code into a Python console:: >>> from rnalysis import gui >>> gui.run_gui() In addition, you can write Python code that uses *RNAlysis* functions as described in the `programmatic interface user guide `_. From sources ------------ The source code for RNAlysis can be downloaded from the `Github repository`_. How to install it ^^^^^^^^^^^^^^^^^ First, clone the public repository: .. code-block:: console $ git clone git://github.com/GuyTeichman/rnalysis Once you have a copy of the source, you can install the basic version of *RNAlysis* with: .. code-block:: console $ python -m pip setup.py install Or you can install the full version of *RNAlysis* with: .. code-block:: console $ python -m pip setup.py install .[all] .. _Github repository: https://github.com/GuyTeichman/RNAlysis How to run it ^^^^^^^^^^^^^ If you installed *RNAlysis* from source, you can open the *RNAlysis* app by executing the command `rnalysis-gui` from your terminal. Alternatively, you can open the *RNAlysis* app by typing the following code into a Python console:: >>> from rnalysis import gui >>> gui.run_gui() In addition, you can write Python code that uses *RNAlysis* functions as described in the `programmatic interface user guide`_.