pennywise 0.0.11

pennywise - A docker based bioinformatics shape shifting tool.

Pennywise

Pennywise has the ability to shapeshift into the bioinformatic tool you are most afraid to install.

Requirements

You must have docker and python3 available at your system.

Install

pip install pennywise 

Usage

List available tools

pennywise list 

Basic usage

pennywise <tool> <regular-tool-options> 

Example 1: Running trimmomatic

pennywise trimmomatic PE r1.fq r2.fq r1_p.fq r1_u.fq r2_p.fq r2_u.fq SLIDINGWINDOW:4:20 MINLEN:100

Example 2: Running spades

pennywise spades -1 r1_p.fq -2 r2_p.fq -o assembly -meta 

First time using a tool

If it's the first time you are running a particular command, pennywise will need to pull the image before it actually runs the tool. Most images will range from 200MB to 2GB, and will get installed in less than 10 minutes providing you have a good internet connection.

pascal@dione:~/Sandbox/$ pennywise quast genome.fa
- It looks like it's your first time running this command!
- pennywise will download the image (staphb/quast:latest) so it can shapeshift
- This can take some time...

Adding your own tools

1. Fork this repository
2. Update pennywise.toml
3. Run pennywise source <your-github-user>

Pennywise will download pennywise.toml from your fork and use it for command reference.

pennywise.toml format

[quast]
image = "staphb/quast:latest"
prefix_cmd = "quast.py"

[prokka]
image = "staphb/prokka:latest"
prefix_cmd = "prokka"

I don't want to use github as source

It's fine, just update ~/.pennywise/pennywise.toml.

Tools Available

• FastANI
• Prokka
• Quast
• Spades
• Trimmomatic