Cutevariant

cutevariant is a light standalone viewer of genetic variation written in Python for Qt. It allows you to view and filter VCF and other format files.

Installation

pip install cutevariant # install
cutevariant             # run

Installation on Windows

Pyside2 is not currently (2019 May) functional on Cygwin, so Cutevariant will not work on Cygwin.

• Install Python3.6+
• Install like the previous chapter said.
• Add the path of python scripts executables to your PATH variable; Something like:

C:\Users\<username>\AppData\Roaming\Python\Python37\Scripts\

Two executables are generated in this directory:

- cutevariant_win_dbg.exe: Open a console in background to see debugging messages.

Note: Qt libs seems to have a very high loglevel and such a verbosity could make the program unusable.

- cutevariant.exe: Standard executable.

Developement in progress

Complete rewriting from Cpp to Python.

To get tests running

git clone git@github.com:labsquare/cutevariant.git
cd cutevariant
virtualenv -p /usr/bin/python3 venv
source venv/bin/activate
make install_deps # install
make install # pip install -e . 
make run     # start application
make test    # start tests

Development & release cycle

Use zest.releaser to handle the version and distribution through pypi.

pip install zest.releaser[recommended]

To yield a new release, use:

fullrelease

Development on Windows (good luck)

• Install Python3.6+

• Install git

• Install make (optional)

  pip install wheel git clone https://github.com/ysard/cutevariant.git git fetch git checkout dev # or devel make install # or pip install --user -e .[dev]

Executable files are located here:

• Executable path: C:\Users<username>\AppData\Roaming\Python\Python37\Scripts\cutevariant.exe

Build standalone program/archive/blob[add synonyms here] on Windows using cx_freeze

Strongly discouraged: You will generate an archive of 350Mo just for a program of less than 900Ko (including 550Ko of fonts and icons).

Install cx_freeze:

pip install cx_freeze

Build a blob:

make build_windows_blob

Your blob is in ./build/ directory.