[Bio-Linux] Have Galaxy in Bio-Linux and usegalaxy.org the same tool installed

[mark fernandes (IFR)]

You may also be able to use that xml list of the URLs to the tools to install them using a Dockerfile like this:
-----------------------------------------------------------
FROM bgruening/galaxy-stable:15.05

MAINTAINER Björn A. Grüning, bjoern.gruening at gmail.com

ENV GALAXY_CONFIG_BRAND GalaxyFlavorGenerator

WORKDIR /galaxy-central

RUN install-repository \ 
	"--url https://testtoolshed.g2.bx.psu.edu/ -o hackdna --name FastQC checker" \ 
	"--url https://testtoolshed.g2.bx.psu.edu/ -o devteam --name Manipulate FASTQ" \ 
	"--url https://testtoolshed.g2.bx.psu.edu/ -o nilesh --name RNASeQC" \ 
	"--url https://testtoolshed.g2.bx.psu.edu/ -o jjohnson --name Trinity read normalization" \ 
	"--url https://testtoolshed.g2.bx.psu.edu/ -o jjohnson --name Trinity" \ 
	"--url https://testtoolshed.g2.bx.psu.edu/ -o boris --name Filter mapped reads" \ 

VOLUME ["/export/", "/data/", "/var/lib/docker"]

EXPOSE :80
EXPOSE :21
EXPOSE :8080

CMD ["/usr/bin/startup"]
------------------------------------------------------
NB Install-repository is a Galaxy script to install tools when building a Galaxy instance.

Hope this helps you along,

Mark Fernandes
Bioinformatics/Biomathematics Training

T: +44 (0)1603 255000
Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK

www.ifr.ac.uk
Facebook | Twitter | LinkedIn | YouTube

The Institute of Food Research receives strategic funding from BBSRC