Installation

Installing Transit2 using Pip

You can use pip to install the TRANSIT package.

> sudo pip3 install transit2

This will automatically download and install TRANSIT as a package (from PyPi), and all remaining required python packages. Once TRANSIT is installed as a package, it can be executed as a command (‘transit’).

Note

If you will be using the pre-processor, TPP, you will also need to install install BWA.

Note

The Transit package will try to install wxPython. If you encounter problems with it, see install wxPython

Note

Note about Python3.12: The update to Python3.12 made changes in the setuptools package that disrupted the installation of Transit as well as other python packages (including some Transit dependencies, like wxPython).

We are working on fixing these problems caused by 3.12. In the meantime, if you have difficulty installing Transit with Python3.12, we recommend trying it with Python3.11, with which Transit should work fine.


Installing Transit2 using Git

Alternatively, TRANSIT2 can be downloaded from the public GitHub server, http://github.com/ioerger/transit2. It is released under a GPL License. An archive with the lastest version of the source code can be downloaded at the following link: Source code.zip

You can clone the git respository as follows:

> git clone https://github.com/ioerger/transit2/

TRANSIT2 is python-based. You must have python3 installed (installed by default on most systems). In addition, TRANSIT relies on some python packages/libraries/modules that you might need to install (see Requirements).

You should be able to run it like this:

> python3 <TRANSIT_PATH>/src/transit.py

If you encounter problems, please contact us or head to the Troubleshooting section.


Requirements

The following libraries/modules are required to run TRANSIT:

All of these dependencies can be installed using the following command.

> pip3 install numpy scipy pillow pypubsub matplotlib statsmodels mne wxPython super_hash ez_yaml

Pip and Python are usually preinstalled in most modern operating systems.


Additional Requirements: R (statistical analysis package)

R is called by Transit for certain commands, such as ZINB, corrplot, and heatmap. As of now, installing R is optional, and requires these additional steps…

Additional Installation Requirements for R:

  • install R (tested on v3.5.2)

  • R packages: MASS, pscl (run “install.packages(MASS)” etc. in R console)

  • Python packages (for python3): rpy2 (v>=3.0) (run “pip3 install rpy2” on command line)

  • Windows users will have to add a system variable for rpy2 to correctly work

  • To set this up, go to Control Panel > System > Advanced system settings > Environment Variables, then add a new variable named R_HOME with the path to your R installation (e.g. C:\Program Files\R\R-4.0.5).

Optional: Install BWA to use with TPP pre-processor

If you will be using the pre-processor, TPP, you will also need to install BWA.

Linux & OSX Instructions

Download the source files:

Extract the files:

> tar -xvjf bwa-0.7.12.tar.bz2

Go to the directory with the extracted source-code, and run make to create the executable files:

> cd bwa-0.7.12
> make

Windows Instructions

For Windows, we provide a windows executable (.exe) for Windows 64 bit:

The 32-bit version of Windows is not recommended as it is limited in the amount of system memory that can be used.


Upgrading

The process of upgrading transit will depend on how you installed transit initially.

Method 1: Upgrading package installation

If you installed TRANSIT as a package, then to upgrade, simply use pip to install tnseq-transit again, but this time include the ‘–upgrade’ flag. For example:

> sudo pip install transit2 --upgrade

This will automatically download and install the latest version of TRANSIT, as well as upgrade any of its requirements if necessary for compatability.

Method 2: Upgrading source installation

If you installed TRANSIT by downloading the raw source, then you can upgrade TRANSIT simply by replacing the old source code with the latest version. You can obtain a .zip archive with the latest version of the source through the following link:

https://github.com/ioerger/transit2/archive/master.zip

Simply extract the code, and replace your existing files or delete the directory with the old source doe and use the newest version.

Or you may perform a ‘git pull’


Note

If an an older version of wxPython is already installed (< 4.0), you may have to remove it and install version 4.0+.


Installing wxPython

wxPython 4+ can be manually installed using pip

> pip3 install wxPython

If the above command fails and you already have wxPython < 4.0 installed, you may have to manually remove it. See https://stackoverflow.com/questions/50688630/cannot-uninstall-wxpython-3-0-2-0-macos for details.

Note

Installing wxPython can be a bit finicky. It might require installing the development version of GTK first. There are at least two versions currently, gtk2 and gtk3. Transit should work with both, although there can be small differences in the visual look of the GUI. To get wxPython to install, you might try doing this:

> sudo apt-get install libgtk-2-dev

or

> sudo apt-get install libgtk-3-dev

depending on which version of libgtk you have installed.

Note

If you are still having problems, another solution might be to install the appropriate version of wxPython directly from the developer’s website. For example, on a recent Linux machine, I had to manually do this step before doing ‘pip install transit2’ (in a fresh virtual environment):

But you might have to adjust the URL to the version specific for your environment.

Troubleshooting

1. No window appears when running in GUI mode.

This problem is likely due to running OSX and previously unsuported versions of matplotlib. Please upgrade matplotlib to the latest version using:

> pip3 install 'matplotlib' --upgrade

2. pip3: SystemError: Cannot compile ‘Python.h’.

This occurs when you do not have the development libraries for python. You can fix this by installing the python-dev packages:

> sudo apt-get install python-dev

3. pip: “The following required packages can not be built: freetype,png,” etc.

This occurs when you do not have some dependencies that are necessary to build some of the python modules TRANSIT requires (usually matplotlib). Installing the following linux dependencies should fix this:

> sudo apt-get install libpng-dev libjpeg8-dev libfreetype6-dev

4. pip3: “No lapack/blas resources found”

This occurs when you do not have some dependencies that are necessary to build some of the python modules TRANSIT requires (usually numpy/scipy). Installing the following linux dependencies should fix this:

> sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran

5. “resources.ContextualVersionConflict (six 1.5.2)…”

This occurs some of the python modules are out of date. You can use pip to upgrade them as follows:

> sudo pip3 install six --upgrade