ummidock/seq_typing repository overview

⁠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

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

# 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]⁠