Kaptive reports information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies. For large-scale analyses, we recommend using Kaptive on the command line, which can be installed via conda, pip or from source.

Kaptive Web is hosted online at kaptive-web.erc.monash.edu - go there to use the web interface, this repository hosts the code used to run the site.

For information on how to install, run, interpret and cite Kaptive please visit the Docs.

A step-by-step tutorial is also available here.

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Installing a Kaptive Web Instance

Would you like to install your own local instance of Kaptive Web? Here's how to do it!

Requirements

• Python >=3.8 with the following modules installed: Kaptive, pygal, pillow, reportlab, lxml.
• These can all be installed with pip or conda:

conda create -y bioconda::kaptive conda-forge::pygal conda-forge::cairosvg conda-forge::pillow conda-forge::reportlab conda-forge::lxml \
-n kaptive_web && conda activate $_

1. Get web2py

You'll need a local copy of web2py. Don't download the web2py app bundle, as that comes with its own copy of Python. We'll instead clone it from GitHub so, we can run it with our copy of Python with the necessary modules installed:

git clone --recursive https://github.com/web2py/web2py.git

2. Get Kaptive Web

We'll put Kaptive Web into web2py's applications directory (and name it 'kaptive_web' because web2py doesn't like dashes in titles) and move to this directory:

git clone https://github.com/klebgenomics/Kaptive-Web web2py/applications/kaptive_web && cd $_

3. Get Kaptive databases

Kaptive comes with reference_databases, however, currently Kaptive-Web needs to parse the reference Genbank to generate the locus images. This isn't ideal, but we can save space by sym-linking Kaptive/reference_databases to web2py/applications/kaptive_web/reference_database like so:

ln -s /path/to/kaptive/install/reference_database /web2py/applications/kaptive_web/

4. Set paths

You now must edit the paths in the settings.ini file (should be in the web2py/applications/kaptive_web directory). Replace /opt/web2py/applications/kaptive_web with full paths (starting with '/') appropriate for your computer.

The settings.ini file should look something like this, but with /opt (the path on my computer) replaced with the path for your web2py:

[Path]
base_path = /opt/web2py/applications/kaptive_web/
reference_database_path = /opt/web2py/applications/kaptive_web/reference_database/
upload_path = /opt/web2py/applications/kaptive_web/uploads/
download_path = /opt/web2py/applications/kaptive_web/downloads/
queue_path = /opt/web2py/applications/kaptive_web/queue/

[General]
job_waiting_time = 60
refresh_waiting_time = 60000

5. Launch web2py

cd ..  # go back to the web2py directory
python web2py.py

A window should pop up asking for a password (you don't need to change anything else). Give it one, and you'll be able to view the web2py interface at http://127.0.0.1:8000.

6. Use Kaptive Web

You'll now be able to use Kaptive Web at http://127.0.0.1:8000/kaptive_web/default/index. You can also get there by going to 'My Sites' in the web2py interface, entering your password, and clicking on 'kaptive_web'.

Enjoy!

Disabling reCAPTCHA

If you are running a local copy of Kaptive Web, you may want to get rid of the reCAPTCHA "I'm not a robot" check.

You can do this by making a couple small modifications to the controllers/default.py file. Specifically, delete the two instances of captcha_field(). Kaptive Web will now assume you're not a robot!