Installation - nselem/corason GitHub Wiki

CORASON modes RAST and gbk

CORASON is available in two modes genbank and RAST files. To install CORASON as presented in "A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data" use the installation guide from BiG-SCAPE CORASON site.

The next steps are the installation guide for CORASON in RAST mode.

CORASON Installation guide

  1. Install docker engine
  2. Download nselem/corason docker-image
  3. Run CORASON

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

1. Install docker engine

CORASON 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
Remember to substitute your-user with your user name Example: nsm@Leia:
User: nsm

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 CORASON images from DockerHub

$ docker pull nselem/corason:latest

Important

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

2 Run CORASON

2.1 Set your database

Create an empty directory that contains your Input Files: RAST-genome data base, Rast_Ids file and file.query
$ mkdir mydir
place inside my dir your files:
mydir.png
GENOMES (dir)
RAST_IDs (tab separated file)
file.query (aminoacid fasta file) Save as many queries as you wish to process.

2.2 Run your docker nselem/corason image

$ docker run -i -t -v /mypath/mydir:/home/output nselem/corason/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
/home/output is fixed at the docker images, you should always use this name.
** on windows ** docker-machine ssh default to be able to share volumes

2.3 Run CORASON inside your docker

$ corason.pl -q yourquery.query -rast_ids yourRAST.Ids -s yourspecial_org 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.

Results.png
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

curl installation

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