docker run -i -t -v $(pwd):/usr/src/CORE nselem/orthocores:latest /bin/bash
Follow the steps, and type the commands into your terminal, do not type $.
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
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/orthocores:latest
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.
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)
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.
$ orthocore.pl -rast_ids yourRAST.Ids
once you finished all your queries exit the container
$ exit
Outputs will be on the new folder /mypath/mydir/query
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
More information about Orthocore in:
[Wiki] (https://github.com/nselem/orthocore/wiki)
$ which curl
$ sudo apt-get update
$ sudo apt-get install curl