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How to build a fresh Docker image from the latest Galaxy

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How to build a fresh Docker image from the latest Galaxy

Md. Rezaul Karim
Hi there,

I was wondering how to build a fresh Docker image/container from the latest version of Galaxy with all the tools available from the tool shed?

Please note that I can build a Docker image for Galaxy by using the following Dockerfile:

# VERSION       0.1
FROM bgruening/galaxy-stable:dev
MAINTAINER Asif Karim<asif.karim.csedu"gmail.com>
ENV GALAXY_CONFIG_BRAND BioOpener
RUN curl -sL https://github.com/bgruening/galaxytools/archive/master.tar.gz | tar xz && cp -r galaxytools-master/visualisations/* config/plugins/visualizations/ && rm -rf ./galaxytools-master
RUN install-biojs msa
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_numpy_1_7" \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_perl_pdf_api2_2_023" \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name infernal --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o biopython --name package_biopython_1_61 --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_trnascan_1_3_1 --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_aragorn_1_2_36 --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name trna_prediction --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o lionelguy --name rnammer --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o bgruening --name rnaz --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name blockclust --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name cofold --panel-section-name RNATools"
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_vienna_rna_1_8" \
    "--url https://toolshed.g2.bx.psu.edu/ -o devteam --name package_bowtie_0_12_7" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name vienna_rna --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_squid_1_9g " \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_randfold_2_0 " \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2_mapper --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2_quantifier --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mirdeep2 --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnashapes --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name suite_mirdeep_2_0" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name antarna --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name dorina --panel-section-id getext" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name compalignp --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnabob --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mafft --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name rnacode --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name gotohscan --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name kinwalker --panel-section-name RNATools"
RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name mea --panel-section-name RNATools" \
    "--url https://toolshed.g2.bx.psu.edu/ -o rnateam --name sortmerna --panel-section-name RNATools"

The Docker image works fine on my machine. However, I'm not sure if I image is built with the latest features of Galaxy.

My second question is can I specify non-shed tools while building the Galaxy Docker image?




Regards,
_________________________________
Md. Rezaul Karim, BSc, MSc
PhD Researcher, INSIGHT Centre for Data Analytics
National University of Ireland, Galway
IDA Business Park, Dangan, Galway, Ireland

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