Installation

TRANSIT can be downloaded from the public GitHub server, http://github.com/mad-lab/transit. It is released under a GPL License. An archive with the lastest version fo the source code can be downloaded at the following link:

Source code.zip

If you know how to utilize git, you can clone the git respository as follows:

git clone https://github.com/mad-lab/transit/

TRANSIT is python-based You must have python 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).

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


Requirements

The following libraries/modules are required to run TRANSIT:

Generally, these requirements are install using the appropriate methods for your operating system, i.e. apt-get or yum for unix machines, pip or easy_install for OSX, or binary installers on Windows. Below more detailed instructions are provided.


Use as a Python Package

TRANSIT can be (optionally) installed as a python package. This can simplify the installation process as it will automatically install most of the requirements. In addition, it will allow users to use some of transit functions in their own scripts if they desire. Below is a brief example of importing transit functions into python. In this example, pair of .wig files are parsed into their read-counts (data) and genomic positions (position), and then normalization factors are calculated. See the documentation of the package for further examples:

Example:
>>> import pytransit.norm_tools as norm_tools
>>> import pytransit.tnseq_tools as tnseq_tools
>>> (data, position) = tnseq_tools.get_data(["transit/data/glycerol_H37Rv_rep1.wig", "transit/data/glycerol_H37Rv_rep2.wig"])
>>> print data
array([[ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.]])
>>> factors = norm_tools.TTR_factors(data)
>>> print factors
array([[ 1.        ],
       [ 0.62862886]])

See also

transit

Detailed Instructions: Linux

Method 1: Install as a Python Package

Most of the requirements are available in default package sources in most Linux distributions. The following commands will install python, pip, wxPython, and several other dependencies needed by the python modules:

#Ubuntu:
sudo apt-get install python python-dev python-pip pkg-config python-wxgtk3.0 libpng-dev libjpeg8-dev libfreetype6-dev

#Fedora:
sudo yum install python python-dev python-pip pkg-config python-wxgtk3.0 libpng-dev libjpeg8-dev libfreetype6-dev

Finally you can use pip to install the TRANSIT package:

sudo pip install tnseq-transit

This will automatically download and install TRANSIT as a package, and all remaining required python packages. Once TRANSIT is installed as a package, it can be executed as

Note

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


Method 2: Install Source Locally

Most of the requirements are available in default package sources in most Linux distributions. The following commands will install python, numpy, scipy, matplotlib on the Ubuntu or Fedora Linux distributions:

#Ubuntu:
sudo apt-get install python python-numpy python-scipy python-matplotlib python-wxgtk3.0

#Fedora:
sudo yum install python numpy scipy python-matplotlib python-wxgtk3.0

The final requirement left to install is Pillow. First you need install pip which simplifies the process of installing certain python modules like Pillow:

#Ubuntu:
sudo apt-get install pip

#Fedora:
sudo yum install pip

Next, using pip you must have a clean installation of Pillow, and the desired libraries. You can achieve this through the following commands:

#Ubuntu:
pip uninstall pillow
pip uninstall Pillow
sudo apt-get install libjpeg-dev zlib1g-dev
pip install -I Pillow

#Fedora:
pip uninstall pillow
pip uninstall Pillow
sudo yum install install libjpeg-dev zlib1g-dev
pip install -I Pillow

After all the requirements have been installed, you can download an archive with the lastest version of the TRANSIT source code through the following link:

Source code.zip

Or, if you prefer to utilize git, you can clone the git respository as follows:

git clone https://github.com/mad-lab/transit/

Note

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


Detailed Instructions: OSX

Method 1: Install as a Python Package

First, download and install the latest Python 2.7.x installation file from the official python website:

Next make sure you have pip installed. Pip can be installed through easy_install, which should come with OSX:

sudo easy_install pip

Download and install the OSX binary of wxpython (cocoa version) for python 2.7:

Note

If you are running OSX El Capitan or later, you will need to use a repackaged version of the wxpython installer. You can download a repackaged version from our servers or you can follow these detailed instructions to repackage the installer if you prefer.

Finally you can use pip to install the TRANSIT package:

sudo pip install tnseq-transit

This will automatically download and install TRANSIT and all remaining requirements.


Note

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


Method 2: Install Source Locally

First, download and install the latest Python 2.7.x installation file from the official python website:

Next make sure you have pip installed. Pip can be installed through easy_install, which should come with OSX:

sudo easy_install pip

Next install numpy, scipy, and matplotlib and pillow using pip:

sudo pip install numpy
sudo pip install scipy
sudo pip install matplotlib
sudo pip install pillow

Download and install the OSX binary of wxpython (cocoa version) for python 2.7:

Note

If you are running OSX El Capitan or later, you will need to use a repackaged version of the wxpython installer. You can download a repackaged version from our servers or you can follow these detailed instructions to repackage the installer if you prefer.

After all the requirements have been installed, you can download an archive with the lastest version of the TRANSIT source code through the following link:

Source code.zip

Or, if you prefer to utilize git, you can clone the git respository as follows:

git clone https://github.com/mad-lab/transit/

Note

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


Detailed Instructions: Windows

Method 1: Install as a Python Package

First, download and install the latest Python 2.7.x installation file from the official python website:

Next, you will need to install pip. If you are using python 2.7.9+ then pip will come pre-installed and included in the default script directory (i.e. C:Python27Scripts ). If you are using python 2.7.8 or older, you will need to manually install pip by downloading and running the get-pip.py script:

python.exe get-pip.py

Make sure that “wheel” is installed. This is necessary to allow you to install .whl (wheel) files:

pip.exe install wheel

Next install the transit package using pip:

pip.exe install tnseq-transit

To use transit in GUI mode you will need to install wxPython versions 3.0 or earlier. We have provided .whl files which you can download and install below. (Note: Make sure to choose the files that match your Windows version i.e. 32/64 bit)

Finally, install the files using pip:

pip.exe install wxPython-3.0.2.0-cp27-none-win_amd64.whl
pip.exe install wxPython_common-3.0.2.0-py2-none-any.whl

making sure to replace the name with the file you downloaded (i.e. 32bit vs 64 bit)

Note

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

Method 2: Install Source Locally

First, download and install the latest Python 2.7.x installation file from the official python website:

Next, you will need to install pip. If you are using python 2.7.9+ then pip will come pre-installed and included in the default script directory (i.e. C:Python27Scripts ). If you are using python 2.7.8 or older, you will need to manually install pip by downloading and running the get-pip.py script:

python.exe get-pip.py

Make sure that “wheel” is installed. This is necessary to allow you to install .whl (wheel) files:

pip.exe install wheel

Download the .whl files for all the requirements (Note: Make sure to choose the files that match your Windows version i.e. 32/64 bit)

Source: These files were obtained from the Unofficial Windows Binaries for Python Extension Packages by Christoph Gohlke, Laboratory for Fluorescence Dynamics, University of California, Irvine.

Finally, install the files using pip:

pip.exe install numpy-1.9.2+mkl-cp27-none-win_amd64.whl
pip.exe install scipy-0.15.1-cp27-none-win_amd64.whl
pip.exe install matplotlib-1.4.3-cp27-none-win_amd64.whl
pip.exe install Pillow-2.8.1-cp27-none-win_amd64.whl
pip.exe install wxPython-3.0.2.0-cp27-none-win_amd64.whl
pip.exe install wxPython_common-3.0.2.0-py2-none-any.whl

After all the requirements have been installed, you can download an archive with the lastest version of the TRANSIT source code through the following link:

Source code.zip

Or, if you prefer to utilize git, you can clone the git respository as follows:

git clone https://github.com/mad-lab/transit/

Note

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


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 tnseq-transit

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/mad-lab/transit/archive/master.zip

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






Troubleshooting


1. Gtk-ERROR **: GTK+ 2.x symbols detected

This error can occur if you have GTK2 already installed and then install wxPython version 3.0+. To fix this, please try installing version 2.8 of wxPython or install a new version of GTK3. More information on this error to come.


2. wxPython & OSX: “The Installer could not install the software because there was no software found to install.”

If you are running OSX El Capitan or later, you will need to use a repackaged version of the wxpython installer as OSX El Capitan has removed support for older packaging methods still used by wxPython. You can download a repackaged version of wxPython from our servers or you can follow these detailed instructions to repackage the installer if you prefer.


3. 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:

pip install 'matplotlib' --upgrade

4. Unable to locate package python-wxgtk3.0

Your version of Linux might not have the repository address that includes python-wxgtk3.0. You can attempt to install version 2.8 instead:

sudo apt-get install python-wxgtk2.8

or you can add the repository that includes version 3.0 and install it:

# Add repo for 14.04
sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu utopic main restricted universe"

#Update repo information
sudo apt-get update

#Install wxPython 3.0
sudo apt-get install python-wxgtk3.0

#Remove repo to prevent version conflicts
sudo add-apt-repository --remove "deb http://archive.ubuntu.com/ubuntu utopic main restricted universe"

5. pip: 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

6. 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

7. pip: “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

8. “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 pip install six --upgrade