Installation

This section of the documentation covers the installation of synthaser.

Python version

synthaser is written using Python 3, and should work with any version above 3.3.

Dependencies

These packages are automatically installed when installing cblaster:

Other dependencies

  • RPS-BLAST is the search tool used in local cblaster searches
  • rpsbproc is used to post-process RPS-BLAST results to remove redundant hits and fill in information about domain families like in the web CD-Search tool

Installation

  1. (Optional) Create a new virtual environment
python3 -m virtualenv venv
source venv/bin/activate

This will create (and activate) a sandboxed environment where you can install Python packages separately to those available on your system. This isn’t necessarily required, but is recommended.

  1. Install synthaser

The easiest way to obtain synthaser is to install it directly from PyPI using pip:

pip install synthaser

This will install synthaser, as well as all of its required dependencies. Alternatively, you could clone the cblaster repository from GitHub and install it like so:

git clone https://www.github.com/gamcil/synthaser
cd synthaser
pip install .

This will download the latest version of cblaster and install it from the downloaded folder, rather than from PyPI.

synthaser should now be available directly on your terminal:

$ synthaser -h
usage: synthaser [-h] [--version] {getdb,getseq,search} ...
synthaser: a Python toolkit for analysing domain architecture of secondary metabolite megasynth (et) ases with NCBI CD-Search.

positional arguments:
  {getdb,getseq,search}
    getdb               Download a CDD database for local searches
    getseq              Download sequences from NCBI
    search              Run a synthaser search

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

Cameron L.M. Gilchrist 2020

Installing RPS-BLAST and rpsbproc

RPS-BLAST is a distributed in the NCBI’s BLAST+ toolkit. This can be acquired either directly from NCBI’s FTP or from your distributions repositories, for example in Ubuntu: sudo apt install ncbi-blast+.

To install rpsbproc, follow these steps:

  1. Acquire the relevant archive for your system from the CDD FTP.
  1. Extract the contents

3. Acquire the data files required by rpsbproc either by running utils/getcdddata.sh, or directly from the FTP as detailed by the README (see: domain-annotation files). The program does NOT require you to download all of the domain databases. So, if doing the former, you can chttps://www.circles.life/au/plan/ancel the run after the necessary files are in data/, then delete db/ and the database .tar.gz files.

4. Make sure the rpsbproc binary file is on your system $PATH. This is a requirement of synthaser, as it will throw an error if it cannot find rpsbproc directly on the $PATH (i.e. accessable in terminal just by typing ‘rpsbproc’).