Installation and preliminary operations

Requirements

Cancermuts is a Python package and requires at minimum Python 3.7 to run. All modern linux distributions and Mac OS include a distribution of Python that you can start using right away.

Furthermore, Cancermuts relies on a number of open source packages, such as:

  • requests

  • bioservices

  • myvariant

  • pyliftover

  • Bio

  • bravado

  • matplotlib

  • pandas

  • parse

  • urllib3

  • future

Please refer to the setup.py file in the distribution for an up to date list of requirements. It should be noted that requirements are installed automatically during the installation process described below.

The installation steps also assume you have either the virtualenv Python package or Conda installed on your system. You can install the virtualenv package by running:

$ python -m pip install --user virtualenv

that should give you access to the virtualenv executable:

$ virtualenv
Running virtualenv with interpreter /usr/bin/python2
You must provide a DEST_DIR
Usage: virtualenv.py [OPTIONS] DEST_DIR
...

if you'd rather use the Conda package manager, you can follow the instructions available on their website

The following instructions are meant for Mac OS or a Linux-based operating system. Cancermuts should also run on Windows, even though it hasn't been tested on it and we currently don't support it. If you want to use Cancermuts on Windows, we recommend doing so through the Windows Subsystem for Linux or by means of a container (e.g. Docker)

Installation procedure

Cancermuts is easily installed as a regular Python package on any supported platform, as follows:

  1. create a local copy of the Cancermuts GitHub repository, in a local folder of your choice:

    mkdir my_cancermuts && cd my_cancermuts
git clone https://github.com/ELELAB/cancermuts.git

  2. in order to install it, we recommend creating a virtual environment for it so that it is isolated from the rest of the system. For instance, using virtualenv package, if available:

    virtualenv -p python3.7 ./cancermuts_env

    another popular choice would be using a conda environment:

    conda create -p cancermuts_env python=3.7

  3. Activate the Python environment, for instance if you used virtualenv:

    source cancermuts_env/bin/activate

    or conda:

    conda activate ./cancermuts_env

    either way you should end up with an active Python environment, i.e. there should be a (cancermuts_env) string before your command prompt:

    teo@my-computer:my_folder$ . cancermuts_env/bin/activate
(cancermuts_env) teo@my-computer:my_folder$

  4. install the package. This should also install all the requirements:

    pip install ./cancermuts

  5. you're now ready to use Cancermuts! In order to use it in the future, you will just need to activate the environment you created following point 3.

You can check if Cancermuts was installed correctly by importing its package from within Python, which shouldn't result in any error:

$ python
Python 3.7.13 (default, Mar 29 2022, 02:18:16)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cancermuts
>>>

You can use cancermuts by means of a Python script or interactively, in a Jupyter notebook or iPython.

Offline resources

COSMIC database

As it will become more clear later, Cancermuts expects some resources to be available on the local computer to be used. Currently, this is only true for the COSMIC Mutant Export, which contains a list of cancer mutations.

In order to obtain it:

  1. head to the COSMIC website, register and log in

  2. head to the Data menu at the top and select the Downloads option

  3. head to the "COSMIC Mutation Data" section and downlaod the corresponding Whole file (CosmicMutantExport.tsv.gz)

  4. decompress the file, e.g. using gzip:

    gunzip -d CosmicMutantExport.tsv.gz

The downloaded file will take a significant amount of disk space, at least 15GB.

Make note of the location of this file as it will come handy in the Tutorial

PhosphositePlus

If you intend to use PhosphoSite Plus as a resource to annotate post-translational modifications you should download its data files so they can be used by Cancermuts, using the following steps:

  1. head to the PhosphoSite Plus website download page

  2. accept the terms and conditions, as adequate

  3. download the files containing the post-translational mutation data in a folder of your choice. Depending on which PTM you're interested it, you might need either (one or more, possibly all):

    • Acetylation_site_dataset.gz

    • Methylation_site_dataset.gz

    • O-GalNAc_site_dataset.gz

    • O-GlcNAc_site_dataset.gz

    • Phosphorylation_site_dataset.gz

    • Sumoylation_site_dataset.gz

  4. decompress all the files, for instance using gzip in Linux or macOS:

    for f in *.gz; do gunzip -d $f; done

  5. Keep note of the location of this directory as it will come handy in the tutorial

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