Installation
This section will help you set up the necessary software and packages required to run SigProfilerTopography.
Prerequisites¶
SigProfilerTopography requires that you have:
- Python version >= 3.4.0
- Internet Connection (for initial installation)
- WGET version 1.9 or RSYNC if you have a firewall
- SigProfilerMatrixGenerator reference genome download
- GRCh37, GRCh38, mm9, mm10, rn6, or 288c.
- Other dependencies and necessary packages are downloaded during the installation.
Upgrades¶
If there is an updated version of the tool that has been released, use the following command within Terminal or the Command Line: pip install SigProfilerTopography --upgrade.This will upgrade the tool to its latest version.
Mac/Unix¶
First, follow the SigProfilerMatrixGenerator Mac guide for installing Python, pip, and a reference genome. Next, follow the download instructions for the latest stable release or the current Github version.
Mac/Unix Stable Release¶
Install SigProfilerTopography using pip.
$ pip install SigProfilerTopography
Mac/Unix Github Release¶
First, clone the Github repository.
$ git clone git@github.com:AlexandrovLab/SigProfilerTopography.git
Next, enter the downloaded directory and install the package.
$ cd SigProfilerTopography
$ pip install .
After SigProfilerTopography successfully installs, the environment is set up and ready to use.
Windows¶
First, follow the SigProfilerMatrixGenerator Windows guide for installing Python, pip, and a reference genome. Next, follow the download instructions for the latest stable release or the current Github version.
Windows Stable Release¶
Install SigProfilerTopography using pip.
$ pip install SigProfilerTopography
Windows Github Release¶
First, clone the Github repository.
$ git clone git@github.com:AlexandrovLab/SigProfilerTopography.git
Next, enter the downloaded directory and install the package.
$ cd SigProfilerTopography
$ pip install .
After SigProfilerTopography successfully installs, the environment is set up and ready to use.