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Merge pull request #14 from ASaiM/asaim-mt
Add ASaiM-MT and update Galaxy to 20.09
2 parents 4945431 + 4f2dc43 commit 2d213a7

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‎Dockerfile‎

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# Galaxy - ASaiM
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FROM quay.io/bgruening/galaxy:17.09
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FROM quay.io/bgruening/galaxy:20.09
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MAINTAINER Bérénice Batut, berenice.batut@gmail.com
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# Enable Conda dependency resolution
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ENV GALAXY_CONFIG_BRAND="ASaiM" \
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GALAXY_CONFIG_CONDA_AUTO_INSTALL=True
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RUN apt update && apt install -y netcat-openbsd
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# Change the tool_conf to get different tool sections and labels
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COPY config/tool_conf.xml $GALAXY_ROOT/config/
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@@ -21,6 +22,8 @@ COPY config/asaim_tools_1.yaml $GALAXY_ROOT/asaim_tools_1.yaml
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COPY config/asaim_tools_2.yaml $GALAXY_ROOT/asaim_tools_2.yaml
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COPY config/asaim_tools_3.yaml $GALAXY_ROOT/asaim_tools_3.yaml
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COPY config/asaim_tools_4.yaml $GALAXY_ROOT/asaim_tools_4.yaml
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COPY config/asaim-mt_tools.yaml $GALAXY_ROOT/asaim-mt_tools.yaml
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COPY config/data_library.yaml $GALAXY_ROOT/data_library.yaml
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RUN df -h && \
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install-tools $GALAXY_ROOT/asaim_tools_1.yaml && \
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/tool_deps/_conda/bin/conda clean --tarballs --yes && \
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install-tools $GALAXY_ROOT/asaim_tools_4.yaml && \
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/tool_deps/_conda/bin/conda clean --tarballs --yes && \
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rm -rf /tool_deps/_conda/pkgs && \
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df -h
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RUN df -h && \
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install-tools $GALAXY_ROOT/asaim-mt_tools.yaml && \
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/tool_deps/_conda/bin/conda clean --tarballs --yes && \
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rm -rf /tool_deps/_conda/pkgs && \
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df -h && \
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mkdir -p $GALAXY_ROOT/workflows
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@@ -49,11 +57,15 @@ ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/top
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ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/general-tutorial/workflows/wgs-worklow.ga $GALAXY_ROOT/workflows/
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ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.ga $GALAXY_ROOT/workflows/
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COPY config/data_managers.yaml $GALAXY_ROOT/data_managers.yaml
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COPY config/data_library.yaml $GALAXY_ROOT/data_library.yaml
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COPY create_admin_user.sh $GALAXY_ROOT/create_admin_user.sh
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ENV GALAXY_CONFIG_TOOL_PATH=/galaxy-central/tools/
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ENV PATH="${PATH}:/tool_deps/_conda/bin"
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RUN startup_lite && \
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galaxy-wait && \
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workflow-install --workflow_path $GALAXY_ROOT/workflows/ -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD
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$GALAXY_ROOT/create_admin_user.sh && \
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workflow-install --publish --workflow_path $GALAXY_ROOT/workflows/ -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_EMAIL -p $GALAXY_DEFAULT_ADMIN_PASSWORD
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#RUN startup_lite && \
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# galaxy-wait && \
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# setup-data-libraries -i $GALAXY_ROOT/data_library.yaml -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD

‎config/asaim-mt_tools.yaml‎

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install_tool_dependencies: True
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install_repository_dependencies: True
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install_resolver_dependencies: True
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tools:
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- name: fastqc
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owner: devteam
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revisions:
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- e7b2202befea
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: cutadapt
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owner: lparsons
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revisions:
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- 49370cb85f0f
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: sortmerna
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owner: rnateam
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revisions:
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- eb35257d2e29
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: fastq_paired_end_interlacer
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owner: devteam
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revisions:
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- 3e396e702cea
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: multiqc
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owner: iuc
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revisions:
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- b2f1f75d49c4
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: metaphlan2
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owner: iuc
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revisions:
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- 8c82c4d90cc6
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: humann2
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owner: iuc
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revisions:
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- b168c0ef3c14
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: metaphlan2krona
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owner: iuc
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revisions:
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- fdbd63e92b01
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: export2graphlan
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owner: iuc
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revisions:
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- ed1becc01910
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: format_metaphlan2_output
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owner: bebatut
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revisions:
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- 2bfa9b200600
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: humann2_renorm_table
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owner: iuc
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revisions:
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- d77397f09da1
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: group_humann2_uniref_abundances_to_go
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owner: bebatut
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revisions:
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- fd2cf7c9d3ec
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: taxonomy_krona_chart
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owner: crs4
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revisions:
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- c9f8fef1df74
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: graphlan_annotate
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owner: iuc
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revisions:
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- 5d6f8f0bef7c
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: humann2_genefamilies_genus_level
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owner: iuc
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revisions:
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- 6d364c65c946
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: combine_metaphlan2_humann2
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owner: bebatut
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revisions:
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- 31394a0c0242
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: humann2_unpack_pathways
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owner: iuc
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revisions:
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- 7f208f1eb64f
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: text_processing
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owner: bgruening
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revisions:
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- 9ff72e942410
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/
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- name: graphlan
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owner: iuc
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revisions:
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- 8f62f666dcb6
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tool_panel_section_label: Tools from workflows
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tool_shed_url: https://toolshed.g2.bx.psu.edu/

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