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Installation
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.
- Install docker engine
- Download nselem/corason docker-image
- Run CORASON
Follow the steps, and type the commands into your terminal, do not type $.
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
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
$ docker pull nselem/corason:latest
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.
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:
GENOMES (dir)
RAST_IDs (tab separated file)
file.query (aminoacid fasta file) Save as many queries as you wish to process.
$ 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
$ corason.pl -q yourquery.query -rast_ids yourRAST.Ids -s yourspecial_org
once you finished all your queries exit the container
$ exit
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
Code and docker file located at:
Code
Docker
$ which curl
$ sudo apt-get update
$ sudo apt-get install curl