Requirements and Installation¶
Requirements¶
gcMapExplorer is written in Python3, therefore, it requires Python3 for installation. It also requires several external Python packages.
Package Required during installation: It has to be installed before gcMapExplorer installation.
Package required after installation: These packages are installed automatically during gcMapExplorer installation.
Package required to install manually:
- PyQt5 - It needs to be installed manually. In case of Python-3.5, it can be installed automatically from PyPI.
Installation Steps on Linux¶
- Python3 is available through package managers such as yum (Fedora, CentOs), YaST (OpenSuse) and apt-get
(Ubuntu, Linux Mint). For example on ubuntu: run
sudo apt-get install python3
command to install Python3. - Install Cython by
pip3 install Cython
command. - Similar to Python3, PyQt5 is available through package managers. For example on ubuntu: run
sudo apt-get install python3-pyqt5
command to install Python3. - Install gcMapExplorer by
pip3 install gcMapExplorer
command.
Installation Steps on MacOS¶
- Python3 is available through Homebrew package manager. After installing Homebrew, run
brew install python3
command to install Python3. - Install Cython by
pip3 install Cython
command. - Similar to Python3, PyQt5 is available through Homebrew . Run
brew install pyqt5 --with-python3
command to install pyqt5. - Install gcMapExplorer by
pip3 install gcMapExplorer
command.
Installation Steps on Windows OS¶
- Download and install WinPython3-Qt5 . Note that WinPython should include PyQt5.
- Open WinPython directory (Default is in C:/ drive) and click on “WinPython Command Prompt”. It will open a command prompt terminal.
- Run
pip install gcMapExplorer
in command prompt terminal to install gcMapExplorer
Note
To execute gcMapExplorer command, simple command prompt terminal (from Start Menu) might not work. Use “WinPython Command Prompt” present in WinPython directory to launch or execute gcMapExplorer.
Updating gcMapExplorer¶
To update the gcMapExplorer package use following command:
pip install --upgrade --no-deps gcMapExplorer
OR
pip3 install --upgrade --no-deps gcMapExplorer
--upgrade
flag is used to update the package and --no-deps
prevents
update of dependent packages like numpy, scipy, matplotlib etc.
Configuring gcMapExplorer¶
- Presently two types of global options are required.
- Scratch Directory to dump intermediate temporary files
- Location to
bigWigInfo
andbigWigToWig
tool
These options are stored in a configuration file. During first use of gcMapExplorer, Scratch Directory is set to
by default temporary directory depending on OS. Location to external tools can be set by either manually opening and
editing configuration file or through gcMapExplorer
Python module (see below).
For quick look to configuration file and cleaning scratch directory, gcMapExplorer config
command can be used:
Configuration using gcMapExplorer
Python modules:
- Print configuration file:
gcMapExplorer.config.printConfig()
- Get configuration as dictionary:
gcMapExplorer.config.getConfig()
- Update configuration file:
gcMapExplorer.config.updateConfig()
- Clean scratch directory:
gcMapExplorer.config.cleanScratch()