Gtnseq/52d032452364master
Gtnseq/
52d032452364master
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/
README.md
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:
2.1 To have the following structure:
root folder |-- group folders |--dataset folders |--fastq files
2.2 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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