GUI to visualize and process variant data
Project description
# 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.
![Cutevariant example](https://raw.githubusercontent.com/labsquare/CuteVariant-cpp/master/screencast.gif)
# 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 ven/bin/activate make install_deps # install make run # start application make test # start tests
### Development & release cycle
Use [zest.releaser](https://zestreleaser.readthedocs.io) 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>AppDataRoamingPythonPython37Scriptscutevariant.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.
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