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Gc3pie app for Tn sequence pipeline

gtn (master)

.gitignore
Dockerfile
README.md
Snakefile
Snakefile_Localhost
enhancer.ch-openrc.sh
gc3pie.conf
gtn.py
install.py
run_gtn.sh

Recent Commits

Commit	Author	Details	Committed
510e350ccc65	DiegoV	changed readme	Jan 14 2019
52d032452364	DiegoV	changed code-blocks syntax	Jan 14 2019
e28baa75ef71	DiegoV	added readme file	Jan 14 2019
c363be7d920e	DiegoV	Added all files necessary to build the docker image	Jan 10 2019
7e46de80fb19	DiegoV	first commit	Jan 10 2019

README.md

Welcome to Gtn: a containerized gc3pie app to run Tnseq pipeline

Requirements

Docker

Root folder data structure:

The root folder that contains the data to be analyzed is expected:

To have the following structure:

root folder
   |-- group folders
       |--dataset folders
          |--fastq files

To adhere to the following naming convention:

A group/sample folder must be named as:

g-{'group_name'}

A dataset folder must be named as:

d{number}-g-{'group_name'}

2 FASTQ files for each dataset are expected to be named as:

d{number}-g-{'group_name'}_R1.fastq
   d{number}-g-{'group_name'}_R2.fastq

Example:

This is a valid root folder (example_data) structure:

example_data/
	├── g-control
	│   └── d1-g-control
	│       ├── d1-g-control_R1.fastq
	│       └── d1-g-control_R2.fastq
	└── g-treated
	     └── d1-g-treated
		├── d1-g-treated_R1.fastq
		└── d1-g-treated_R2.fastq

Run gtn

Cloud infrastructure (UZH only)

$ docker run -it -v /path/to/input/:/input -v /path/to/output/:/output -v /path/to/.ssh:/root/.ssh sparkvilla/tnseq

Localhost

$ docker run -it -v /path/to/input/:/input -v /path/to/output/:/output sparkvilla/tnseq localhost

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