nselem/orthocores repository overview

docker run -i -t -v $(pwd):/usr/src/CORE nselem/orthocores:latest /bin/bash

⁠orthoCORE Installation guide

1. Install docker engine
2. Download nselem/orthocore docker-image
3. Run orthoCORE

Follow the steps, and type the commands into your terminal, do not type $.

⁠1. Install docker engine

orthoCORE runs on docker, if you have docker engine installed skip this step. This are Linux minimal docker installation guide, if you don't use Linux or you look for a detailed tutorial on Linux/Windows/Mac Docker engine installation please consult Docker getting Starting⁠.

$ curl -fsSL https://get.docker.com/ | sh
*if you don’t have curl search on this document curl installation
Then type:
$ sudo usermod -aG docker your-user

⁠Important step:

Log out from your ubuntu session (restart your machine) and get back in into your user session before the next step. You may need to restart your computer and not just log out from your session in order to changes to take effect.

Test your docker engine with the command:
$ docker run hello-world

⁠1 Download ORTHOCORE images from DockerHub

$ docker pull nselem/orthocores:latest

⁠Important

docker pull may be slow depending on your internet connection, because nselem/evodivmet docker-image is being downloaded, its only this time won’t happen again.

⁠2 Run ORTHOCORE

⁠2.1 Set your database

Create an empty directory that contains your:
RAST-genome data base, Rast_Ids file
$ mkdir mydir
place your files inside mydir:

` GENOMES   (dir)   RAST_IDs (tab separated file)

⁠2.2 Run your docker nselem/evodivmet image  

cd /mypath/mydir   $ docker run -i -t -v $(pwd):/usr/src/CORE nselem/orthocores:latest /bin/bash

/mypath/mydir/ is your local directory were you store your inputs, can have any name you choose.
Use absolute paths, if you don’t know the path to your dir, place yourself on your directory and type on the terminal
$ pwd
/usr/src/CORE is fixed at the docker images, you should always use this name.

⁠2.3 Run ORTHOCORE inside your docker

$ orthocore.pl -rast_ids yourRAST.Ids once you finished all your queries exit the container
$ exit

⁠2.4 Read your results !

Outputs will be on the new folder /mypath/mydir/query

• query.svg SVG file with clusters similar to you query sorted phylogenetically
• query_Report Functional cluster genomic core report.
• *.tre Phylogenetic tree of the genomic cluster core.

On this example query file was yourquery.query and input directory was /home/mydir, output files are located on /home/mydir/yourquery

⁠Links

Code and docker file located at:
Code⁠
Docker⁠
More information about Orthocore in:
[Wiki] (https://github.com/nselem/orthocore/wiki⁠)

⁠curl installation

• $ which curl
• $ sudo apt-get update
• $ sudo apt-get install curl

⁠To do list

• Create a direct access with Logo
• Redirect process to a different folder so multiple runs can be performed without data mess
• [1/2] Write the tutorial
• Write a myRast Docker file
• Learn Docker-Apache to link with Evomining
• Test with many users