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">
RUN curl -sL | tar xz && cp -r galaxytools-master/visualisations/* config/plugins/visualizations/ && rm -rf ./galaxytools-master
RUN install-biojs msa
RUN install-repository \
    "--url -o iuc --name package_numpy_1_7" \
    "--url -o iuc --name package_perl_pdf_api2_2_023" \
    "--url -o bgruening --name infernal --panel-section-name RNATools" \
    "--url -o biopython --name package_biopython_1_61 --panel-section-name RNATools" \
    "--url -o iuc --name package_trnascan_1_3_1 --panel-section-name RNATools" \
    "--url -o iuc --name package_aragorn_1_2_36 --panel-section-name RNATools" \
    "--url -o bgruening --name trna_prediction --panel-section-name RNATools" \
    "--url -o lionelguy --name rnammer --panel-section-name RNATools" \
    "--url -o bgruening --name rnaz --panel-section-name RNATools" \
    "--url -o rnateam --name blockclust --panel-section-name RNATools" \
    "--url -o rnateam --name cofold --panel-section-name RNATools"
RUN install-repository \
    "--url -o iuc --name package_vienna_rna_1_8" \
    "--url -o devteam --name package_bowtie_0_12_7" \
    "--url -o rnateam --name vienna_rna --panel-section-name RNATools" \
    "--url -o iuc --name package_squid_1_9g " \
    "--url -o iuc --name package_randfold_2_0 " \
    "--url -o rnateam --name mirdeep2_mapper --panel-section-name RNATools" \
    "--url -o rnateam --name mirdeep2_quantifier --panel-section-name RNATools" \
    "--url -o rnateam --name mirdeep2 --panel-section-name RNATools" \
    "--url -o rnateam --name rnashapes --panel-section-name RNATools" \
    "--url -o rnateam --name suite_mirdeep_2_0" \
    "--url -o rnateam --name antarna --panel-section-name RNATools" \
    "--url -o rnateam --name dorina --panel-section-id getext" \
    "--url -o rnateam --name compalignp --panel-section-name RNATools" \
    "--url -o rnateam --name rnabob --panel-section-name RNATools" \
    "--url -o rnateam --name mafft --panel-section-name RNATools" \
    "--url -o rnateam --name rnacode --panel-section-name RNATools" \
    "--url -o rnateam --name gotohscan --panel-section-name RNATools" \
    "--url -o rnateam --name kinwalker --panel-section-name RNATools"
RUN install-repository \
    "--url -o rnateam --name mea --panel-section-name RNATools" \
    "--url -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?

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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