Installation

The code for itpseq is available on GitHub (t-renault/itpseq) under an GPL-3.0 open source license.

We assume that Python and the pip package manager are already installed on your machine.

The itpseq module and its command line tools can be installed/updated from PyPI by running the following command:

pip install -U itpseq

This should make the itpseq command available in your shell, as well as a python module.

In order to check the correct installation, run:

itpseq --help

which should output the help page:

Usage: itpseq [OPTIONS] COMMAND [ARGS]...

  itpseq - A command-line tool for the analysis of iTP-Seq data.

Options:
  -v, --version  Show the version and exit.
  -h, --help     Show this message and exit.

Commands:
  help    Open the HTML documentation in the default web browser.
  parse   Parse and filter the assembled iTP-Seq FASTQ files to produce...
  report  Generate a report for the dataset in the specified DIRECTORY.

  To get help on a specific command, run: itpseq COMMAND --help

From within a python interpreter or python script:

In [1]: import itpseq

In [2]: print(itpseq.__version__)
0.0.1a8