Docker

INNUca.py - Docker

INNUca - Reads Control and Assembly

INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search

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

https://hub.docker.com/r/ummidock/innuca

This is a dockerfile for using INNUca, with all dependencies already installed.

Within this container you can find:

• Debian Stretch (9)
• Perl v5.30.1
• git v2.11.0
• Python v2.7
• Java-JDK v1.8.0_40 headless
• Blast+ v2.9.0
• mlst v2.18.1
• ReMatCh v4.1.0
• Kraken v2.0.7
• INNUca v4.2.2

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/innuca:4.2.2-02

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/innuca:4.2.2-02

Using GitHub (build docker image)

1. git clone https://github.com/B-UMMI/INNUca.git
2. docker build -t ummidock/innuca:4.2.2-02 ./INNUca/Docker/

Run (using automated build image)

docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/fastq_data:/data/ ummidock/innuca:4.2.2-02 INNUca.py --speciesExpected "Streptococcus agalactiae" --genomeSizeExpectedMb 2.1 --inputDirectory /data/ --outdir /data/innuca_output/ --threads 8 --maxNumberContigs 100

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/innuca:4.2.2-02

# Create container (only needed to be done once)
udocker create --name=innuca_4-2-2_02 ummidock/innuca:4.2.2-02

# Run INNUca
udocker run --user $(id -u):$(id -g) -v /local/folder/fastq_data:/data/ innuca_4-2-2_02 INNUca.py --speciesExpected "Streptococcus agalactiae" --genomeSizeExpectedMb 2.1 --inputDirectory /data/ --outdir /data/innuca_output/ --threads 8 --maxNumberContigs 100

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).

Updating the mlst database in docker instance

After you've built the docker image, you can still update the mlst database. For this, the update_mlst_db.sh script is provided. Simply run in after initiating the instance with:

/NGStools/INNUca/Docker/update_mlst_db.sh

For more information on this please consult the provided information in the mlst page.

Contact

Miguel Machado mpmachado@medicina.ulisboa.pt
Catarina Mendes cimendes@medicina.ulisboa.pt