README.md

seq_typing - Docker

seq_typing - Determines which reference sequence is more likely to be present in a given sample

https://github.com/B-UMMI/seq_typing

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This is a Dockerfile to produce a seq_typing image, with all dependencies already installed.

Within this image you can find:

• ubuntu:16.04
• git v2.7.4
• Python v2.7.12 and v3.5.2
• Blast+ v2.7.1
• ReMatCh v4.0.1
• seq_typing v2.3

Using play-with-docker

Within play-with-docker webpage click on create session. Then, another page will open with a big counter on the upper left corner. Click on + add new instance and a terminal like instance should be generated on the right. On this terminal you can load this docker image as follows:

docker pull ummidock/seq_typing:2.3-01

Build this docker on your local machine

For this, docker needs to be installed on your machine. Instructions for this can be found here.

Using DockerHub (automated build image)

docker pull ummidock/seq_typing:2.3-01

Using GitHub (build docker image)

1. git clone https://github.com/B-UMMI/seq_typing.git
2. docker build -t ummidock/seq_typing:2.3-01 ./seq_typing/Docker/

Run (using automated build image)

Example of Haemophilus influenzae serotyping using reads and provided references sequences (adapted from here).

docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/fastq_data:/data/ ummidock/seq_typing:2.3-01 \
    seq_typing.py reads --org Haemophilus influenzae \
                        --fastq /data/sample_1.fq.gz /data/sample_2.fq.gz \
                        --outdir /data/sample_out/ \
                        --threads 2

For more examples on how to run seq_typing without a Docker container see general README file.

udocker

"A basic user tool to execute simple docker containers in user space without requiring root privileges.". From here.

# Get Docker image
udocker pull ummidock/seq_typing:2.3-01

# Create container (only needed to be done once)
udocker create --name=seq_typing_2-3_01 ummidock/seq_typing:2.3-01

# Run seq_typing
udocker run --user $(id -u):$(id -g) -v /local/folder/fastq_data:/data/ seq_typing_2-3_01 \
    seq_typing.py reads --org Haemophilus influenzae \
                        --fastq /data/sample_1.fq.gz /data/sample_2.fq.gz \
                        --outdir /data/sample_out/ \
                        --threads 2

More examples on how to use udocker can be found in udocker GitHub page

NOTE: if some Error: in download: HTTP/1.1 400 Bad Request occur while pulling the Docker image, first pull it using docker and then retry pulling it with udocker (same with Shifter).

Contact

Miguel Machado [email protected]