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Last pushed: 2 months ago
Short Description
Test version of INNUca's docker integration.
Full Description

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

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

Within this container you can find:

  • ubuntu:16.04
  • git
  • python-dev (version 2.x)
  • wget
  • openjdk-8-jre
  • ncbi-blast version 2.6.0
  • libmoo-perl liblist-moreutils-perl
  • mlst
  • INNUca

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:

1) docker pull cimendes/innuca
2) docker run -it cimendes/innuca bash

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

1) docker pull cimendes/innuca

To run, do
2) docker run -it cimendes/innuca bash

Using GitHub

1) git clone https://github.com/cimendes/INNUca.git
2) docker build . INNUca

To run, do
3) docker run -it INNUca bash

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

Catarina Mendes
cimendes@medicina.ulisboa.pt

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