Installation

Remember – pyGenomeTracks is available for command line usage as well as for integration into Galaxy servers!

Requirements

Python dependencies:

• Python >= 3.8

• numpy >= 1.20

• intervaltree >= 2.1.0

• pyBigWig >= 0.3.16

• hicmatrix >= 15

• pysam >= 0.14

• matplotlib >= 3.1.1,<= 3.6.2

• gffutils >= 0.9

• pybedtools >= 0.8.1

• tqdm >= 4.20

• bx-python >=0.8.13

• pyfaidx >= 0.1.3

External dependencies:

• BEDTools

Command line installation using conda

We encourage users to use conda installation to install pygenometracks. All of the requirements for pyGenomeTracks can be installed via Anaconda with:

$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks

To get a specific version, one can specify it. For example:

$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7

Command line installation using conda and mamba

However, we noticed that conda installation can be quite slow so using mamba can help. You first need to create the environment and install mamba:

$ conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.9

Then activate the environment and install pygenometracks with mamba:

$ conda activate pygenometracks
$ mamba install -c conda-forge -c bioconda pygenometracks

or if you want a specific version:

$ conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
$ conda activate pygenometracks
$ mamba install -c conda-forge -c bioconda pygenometracks=3.5

Command line installation using pip

Install pyGenomeTracks using the following command:

$ pip install pyGenomeTracks

All python requirements should be automatically installed.

Since version 3.5, pyGenomeTracks require BEDTools, do not forget to install it or load it into your environment.

If you need to specify a specific path for the installation of the tools, make use of pip install’s numerous options:

$ pip install --install-option="--prefix=/MyPath/Tools/pyGenomeTracks" git+https://github.com/deeptools/pyGenomeTracks.git

Command line installation without pip

You are highly recommended to use conda install rather than the following complicated steps.

1. Install the requirements listed above in the “requirements” section. This is done automatically by pip (except BEDTools).

2. Download source code

$ git clone https://github.com/deeptools/pyGenomeTracks.git

or if you want a particular release, choose one from https://github.com/deeptools/pygenometracks/releases:

$ wget https://github.com/deeptools/pyGenomeTracks/archive/3.1.tar.gz
$ tar -xzvf

3. install the source code (if you don’t have root permission, you can set a specific folder using the --prefix option)

$ python setup.py install --prefix /User/Tools/pyGenomeTracks3.1

Galaxy installation

pyGenomeTracks can be easily integrated into a local Galaxy. The wrapper and its dependencies are available in the Galaxy Tool Shed.

Installation via Galaxy API (recommended)

First generate an API Key for your admin user and run the the installation script:

$ python ./scripts/api/install_tool_shed_repositories.py \
        --api YOUR_API_KEY -l http://localhost/ \
        --url http://toolshed.g2.bx.psu.edu/ \
        -o iuc -r <revision> --name pygenometracks \
        --tool-deps --repository-deps --panel-section-name plots

The -r argument specifies the version of pygenometracks.

You can watch the installation status under: Top Panel –> Admin –> Manage installed tool shed repositories

Installation via web browser

• go to the admin page

• select Search and browse tool sheds

• Galaxy tool shed –> Visualization –> pygenometracks

• install pygenometracks