Installation

First time installation

We recommend installing this tool on Linux or macOS using the Conda packaging system, via the BioConda channel, which will handle all the dependencies:

$ conda install thapbi_pict

Alternatively, since the software is on the Python Package Index (PyPI), the following command will install it along with its Python dependencies:

$ pip install thapbi_pict

However, in this case you will still need to install at least the command line tool flash (for merging Illumina paired reads), and optionally others like NCBI BLAST+ (used for one classifier method). If you have BioConda setup, use the following:

$ conda install --file requirements-ext.txt

If you are not using Conda, then on a typical Linux system most of the tools required will be available via the default distribution packages, although not always under the same package name.

On Debian (with the efforts of DebianMed), or Ubuntu Linux, try:

$ sudo apt-get install ncbi-blast+

If you are on Windows, and do not wish to or cannot use the Windows Subsystem for Linux (WSL), the tool can be installed with pip, but you will have to manually install the command line dependencies. Download a pre-compiled binary from https://ccb.jhu.edu/software/FLASH/ and BLAST+ (if required) from the NCBI, and ensure they are on the system PATH. To run the test suite and worked example scripts, you will also need a bash shell with basic Unix tools like grep.

If you want to install the very latest unreleased code, you must download the source code from the repository on GitHub - see the CONTRIBUTING.rst file for more details.

Once installed, you should be able to run the tool using:

$ thapbi_pict

This should automatically find the installed copy of the Python code. Use thapbi_pict -v to report the version, or thapbi_pict -h for help.

Updating

If you installed via conda, this should work:

$ conda update thapbi-pict

If you installed via pip, this should work:

$ pip install --upgrade thapbi-pict

Either way, you can check the installed tool version using:

$ thapbi_pict -v