kmerspectrumanalyzer's Introduction

MG-RAST source code

This is the repository for the MG-RAST metagenome analysis system. Take a look at MG-RAST.

WARNING

Don't try this at home.

LICENSE

MG-RAST is made available under a BSD type LICENSE, see the LICENSE file for details.

Please note: The MG-RAST team is dedicated to supporting the

server at http://www.mg-rast.org, we are not resourced to help with local installations. So as much as we'd like to we can't help with local installations of this software.

REQUIREMENTS

Hardware

MG-RAST is a pipeline, an archive, a complex web interface and several other tools. The entire systems was designed for a Linux/Unix system. We run it on a dedicated small cluster for the server infrastructure and heavily utilize CLOUD computing resources.

Systems-Software

MySQL
Cassandra
Perl
Python
R
Apache
NGINX

For the bioinformatics software and databases used in MG-RAST please see our manual: http://help.mg-rast.org

INSTRUCTIONS

type make

API server

Build image and push to dockerhub:

git clone https://github.com/MG-RAST/MG-RAST.git
cd MG-RAST
docker build -t mgrast/api-server:dev .

docker push mgrast/api-server:dev

Get config: (private mcs git repo, for details see fleet unit)

if cd /home/core/mgrast-config; then git pull; else cd /home/core/ ; git clone [email protected]:mgrast-config.git ; fi

Download data

docker run -t -i --name api -v /media/ephemeral/api-server-data:/m5nr mgrast/api /MG-RAST/bin/download_m5nr_blast.sh
docker rm api

Start container:

docker run -t -i --name api  -v /home/core/mgrast-config/services/api-server:/api-server-conf -v /media/ephemeral/api-server-data:/m5nr -p 80:80 mgrast/api-server /usr/local/apache2/bin/httpd -DFOREGROUND -f /MG-RAST/conf/httpd.conf

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