├── .dockerignore ├── .gitignore ├── .travis.yml ├── Dockerfile ├── LICENSE ├── README.md ├── bin └── run_data_managers ├── config ├── asaim-mt_tools.yaml ├── asaim_logo.svg ├── asaim_tools_1.yaml ├── asaim_tools_2.yaml ├── asaim_tools_3.yaml ├── asaim_tools_4.yaml ├── data_library.yaml ├── data_managers.yaml ├── tool_conf.xml ├── welcome.html └── workflows │ ├── EBI_Metagenomics_workflow_3.0.ga │ ├── asaim-mt_workflow.ga │ ├── megahit_assembly.ga │ ├── metaspades_assembly.ga │ ├── qiime_illumina_overview_tutorial.ga │ ├── shotgun_workflow.ga │ ├── shotgun_workflow_pe.ga │ ├── shotgun_workflow_pe_collection.ga │ └── shotgun_workflow_se_collection.ga └── create_admin_user.sh /.dockerignore: -------------------------------------------------------------------------------- 1 | README.md 2 | LICENSE 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | 3 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | sudo: required 2 | language: minimal 3 | python: 2.7 4 | 5 | services: 6 | - docker 7 | 8 | env: 9 | - TOX_ENV=py27 10 | 11 | git: 12 | submodules: false 13 | 14 | before_install: 15 | - set -e 16 | - rm -rf /home/travis/perl5/ /home/travis/.phpenv /home/travis/gopath /home/travis/otp /home/travis/.gimme/ /home/travis/.rvm /home/travis/.nvm 17 | - sudo rm -rf /usr/local/clang* 18 | - wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile 19 | # As Travis VM is limited to 30Go, we remove all conda envs once they are installed successfully to free some disk space (see #23) 20 | - sed -i 's|\(install-tools.*&&\) \\|\1 rm \-rf /tool_deps/_conda/envs/* \&\& \\|g' Dockerfile 21 | - make docker_install 22 | # Next line is an alternative to travis_wait that allows to keep the logs from make docker_build 23 | - while sleep 9m; do echo "[TRAVIS] Still running..."; done & 24 | - make docker_build 25 | - make docker_run 26 | - sleep 300 27 | 28 | install: 29 | - make install 30 | 31 | script: 32 | - make test_api 33 | - make test_ftp 34 | - make test_bioblend 35 | #- make test_docker_in_docker 36 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | # Galaxy - ASaiM 2 | FROM quay.io/bgruening/galaxy:20.09 3 | 4 | MAINTAINER Bérénice Batut, berenice.batut@gmail.com 5 | 6 | # Enable Conda dependency resolution 7 | ENV GALAXY_CONFIG_BRAND="ASaiM" \ 8 | GALAXY_CONFIG_CONDA_AUTO_INSTALL=True 9 | 10 | RUN apt update && apt install -y netcat-openbsd 11 | # Change the tool_conf to get different tool sections and labels 12 | COPY config/tool_conf.xml $GALAXY_ROOT/config/ 13 | 14 | # Install tools 15 | # Split into multiple layers to minimize disk space usage while building 16 | # Rules to follow: 17 | # - Keep in the same yaml file the tools that share common conda dependencies (conda is only able to use hardlinks within a Docker layer) 18 | # - Docker will use 2*(size of the layer) on the disk while building, so 1 yaml should not install more data than half of the remaining space on the disk 19 | # => 'big' tools should go in the first yaml file, the last yaml file should contain smaller tools 20 | # - When one of the layer can't be built with a "no space left" error message, you'll probably need to split a yaml in 2 (supposing you followed the previous rules) 21 | COPY config/asaim_tools_1.yaml $GALAXY_ROOT/asaim_tools_1.yaml 22 | COPY config/asaim_tools_2.yaml $GALAXY_ROOT/asaim_tools_2.yaml 23 | COPY config/asaim_tools_3.yaml $GALAXY_ROOT/asaim_tools_3.yaml 24 | COPY config/asaim_tools_4.yaml $GALAXY_ROOT/asaim_tools_4.yaml 25 | COPY config/asaim-mt_tools.yaml $GALAXY_ROOT/asaim-mt_tools.yaml 26 | COPY config/data_library.yaml $GALAXY_ROOT/data_library.yaml 27 | RUN df -h && \ 28 | install-tools $GALAXY_ROOT/asaim_tools_1.yaml && \ 29 | /tool_deps/_conda/bin/conda clean --tarballs --yes && \ 30 | rm -rf /tool_deps/_conda/pkgs && \ 31 | df -h 32 | RUN df -h && \ 33 | install-tools $GALAXY_ROOT/asaim_tools_2.yaml && \ 34 | /tool_deps/_conda/bin/conda clean --tarballs --yes && \ 35 | rm -rf /tool_deps/_conda/pkgs && \ 36 | df -h 37 | RUN df -h && \ 38 | install-tools $GALAXY_ROOT/asaim_tools_3.yaml && \ 39 | /tool_deps/_conda/bin/conda clean --tarballs --yes && \ 40 | rm -rf /tool_deps/_conda/pkgs && \ 41 | df -h 42 | RUN df -h && \ 43 | install-tools $GALAXY_ROOT/asaim_tools_4.yaml && \ 44 | /tool_deps/_conda/bin/conda clean --tarballs --yes && \ 45 | rm -rf /tool_deps/_conda/pkgs && \ 46 | df -h 47 | RUN df -h && \ 48 | install-tools $GALAXY_ROOT/asaim-mt_tools.yaml && \ 49 | /tool_deps/_conda/bin/conda clean --tarballs --yes && \ 50 | rm -rf /tool_deps/_conda/pkgs && \ 51 | df -h && \ 52 | mkdir -p $GALAXY_ROOT/workflows 53 | 54 | # Import workflows (local and from training) and data manager description, install the data libraries and the workflows 55 | COPY config/workflows/* $GALAXY_ROOT/workflows/ 56 | ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/general-tutorial/workflows/wgs-worklow.ga $GALAXY_ROOT/workflows/ 57 | ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/general-tutorial/workflows/wgs-worklow.ga $GALAXY_ROOT/workflows/ 58 | ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.ga $GALAXY_ROOT/workflows/ 59 | COPY config/data_managers.yaml $GALAXY_ROOT/data_managers.yaml 60 | 61 | COPY create_admin_user.sh $GALAXY_ROOT/create_admin_user.sh 62 | 63 | ENV GALAXY_CONFIG_TOOL_PATH=/galaxy-central/tools/ 64 | ENV PATH="${PATH}:/tool_deps/_conda/bin" 65 | RUN startup_lite && \ 66 | galaxy-wait && \ 67 | $GALAXY_ROOT/create_admin_user.sh && \ 68 | workflow-install --publish --workflow_path $GALAXY_ROOT/workflows/ -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_EMAIL -p $GALAXY_DEFAULT_ADMIN_PASSWORD 69 | #RUN startup_lite && \ 70 | # galaxy-wait && \ 71 | # setup-data-libraries -i $GALAXY_ROOT/data_library.yaml -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD 72 | 73 | 74 | # Copy the script to launch the data managers 75 | COPY bin/run_data_managers run_data_managers 76 | 77 | # Install the tours 78 | ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/general-tutorial/tours/metagenomics-general-tutorial-amplicon.yml $GALAXY_ROOT/config/plugins/tours/ 79 | ADD https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/metagenomics/tutorials/general-tutorial/tours/metagenomics-general-tutorial-shotgun.yml $GALAXY_ROOT/config/plugins/tours/ 80 | 81 | # Add Container Style 82 | ENV GALAXY_CONFIG_WELCOME_URL=$GALAXY_CONFIG_DIR/web/welcome.html 83 | COPY config/welcome.html $GALAXY_CONFIG_DIR/web/welcome.html 84 | COPY config/asaim_logo.svg $GALAXY_CONFIG_DIR/web/welcome_asaim_logo.svg 85 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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We also recommend that a 185 | file or class name and description of purpose be included on the 186 | same "printed page" as the copyright notice for easier 187 | identification within third-party archives. 188 | 189 | Copyright (2015) 190 | 191 | Licensed under the Apache License, Version 2.0 (the "License"); 192 | you may not use this file except in compliance with the License. 193 | You may obtain a copy of the License at 194 | 195 | http://www.apache.org/licenses/LICENSE-2.0 196 | 197 | Unless required by applicable law or agreed to in writing, software 198 | distributed under the License is distributed on an "AS IS" BASIS, 199 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 200 | See the License for the specific language governing permissions and 201 | limitations under the License. 202 | 203 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ASaiM framework 2 | =============== 3 | 4 | [![Docker Repository on Quay](https://quay.io/repository/bebatut/asaim-framework/status "Docker Repository on Quay")](https://quay.io/repository/bebatut/asaim-framework) 5 | 6 | ASaiM framework is an open-source opinionated Galaxy-based framework. It integrates tools, specifically chosen for metagenomic and metatranscriptomic studies and hierarchically organized to orient user choice toward the best tool for a given task. 7 | 8 | Details about this framework is available on a dedicated documentation available at [http://asaim.readthedocs.org/](http://asaim.readthedocs.org/). 9 | 10 | This framework is using the [Galaxy Docker](http://bgruening.github.io/docker-galaxy-stable/) to ease the deployment the Galaxy instance. 11 | 12 | # Usage 13 | 14 | ## Requirements 15 | 16 | To use the ASaiM framework, [Docker](https://www.docker.com/products/overview#h_installation) is required 17 | 18 | For Linux users and people familiar with the command line, please follow the [very good instructions](https://docs.docker.com/installation/) from the Docker project. Non-Linux users are encouraged to use [Kitematic](https://kitematic.com), a graphical User-Interface for managing Docker containers. 19 | 20 | > The databases used by HUMAnN2 are quite big, we recommend to have at least 100 Gb of disk space 21 | 22 | ## ASaiM launch 23 | 24 | 1. Starting the ASaiM Docker container: analogous to starting the generic Galaxy Docker image: 25 | 26 | ``` 27 | $ docker run -d -p 8080:80 quay.io/bebatut/asaim-framework 28 | ``` 29 | 30 | Nevertheless, here is a quick rundown: 31 | 32 | - `docker run` starts the Image/Container 33 | 34 | In case the Container is not already stored locally, Docker downloads it automatically 35 | 36 | - The argument `-p 8080:80` makes the port 80 (inside of the container) available on port 8080 on your host 37 | 38 | Inside the container a Apache web server is running on port 80 and that port can be bound to a local port on your host computer. 39 | With this parameter you can access your Galaxy instance via `http://localhost:8080` immediately after executing the command above 40 | 41 | - `quay.io/bebatut/asaim-framework` is the Image/Container name, that directs Docker to the correct path in the [Docker index](https://index.docker.io/u/bgruening/galaxy-rna-workbench/) 42 | - `-d` will start the Docker container in Daemon mode. 43 | 44 | > A detailed discussion of Docker's parameters is given in the [Docker manual](http://docs.docker.io/). It is really worth reading. 45 | 46 | The Docker container is run: Galaxy will be launched! 47 | 48 | > Setting up Galaxy and its components can take several minutes. You can inspect the state of the starting using: 49 | > ``` 50 | > $ docker ps # to obtain the id of the container 51 | > $ docker logs 52 | > ``` 53 | 54 | The previous commands will start the ASaiM framework with the configuration and launch of a Galaxy instance and its population with the needed tools, workflows and databases. The instance will be accessible at [http://localhost:8080](http://localhost:8080). 55 | 56 | 2. Installation of the databases once Galaxy is running 57 | 58 | ``` 59 | $ docker exec ./run_data_managers 60 | ``` 61 | 62 | ## Usage: workflows, databases, data, etc. 63 | 64 | More details about the installation of ASaiM and its usage can be found on the [online documentation](http://asaim.readthedocs.io/en/latest/installation.html) 65 | 66 | # Documentation 67 | 68 | Available tools and workflows in ASaiM framework are described in the documentation available at [http://asaim.readthedocs.org/](http://asaim.readthedocs.org/en/latest/framework/index.html). It comes also with tutorials. 69 | 70 | # Bug Reports 71 | 72 | Any bug can be filed in an issue [here](https://github.com/ASaiM/framework/issues). 73 | 74 | # License 75 | 76 | ASaiM framework is released under Apache 2 License. See the [LICENSE](LICENSE) file for details. 77 | 78 | # Contributing 79 | 80 | How to Contribute: 81 | 82 | - Make sure you have a [GitHub account](https://github.com/signup/free) 83 | - Make sure you have git [installed](https://help.github.com/articles/set-up-git) 84 | - Fork the repository on [GitHub](https://github.com/galaxyproject/tools-iuc/fork) 85 | - Make the desired modifications - consider using a [feature branch](https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches) 86 | - Open a [pull request](https://help.github.com/articles/using-pull-requests) with these changes. 87 | 88 | Thanks! 89 | 90 | # Citation 91 | 92 | If you use this tool, please cite: 93 | 94 | ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota 95 | Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret 96 | bioRxiv 183970; doi: https://doi.org/10.1101/183970 97 | -------------------------------------------------------------------------------- /bin/run_data_managers: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | # Launch the data managers to install the databases 3 | 4 | echo "Launch the data managers" 5 | run-data-managers \ 6 | --config $GALAXY_ROOT/data_managers.yaml \ 7 | -g "http://localhost:80" \ 8 | -u $GALAXY_DEFAULT_ADMIN_USER \ 9 | -p $GALAXY_DEFAULT_ADMIN_PASSWORD 10 | 11 | echo "Restart Galaxy" 12 | supervisorctl restart galaxy: 13 | -------------------------------------------------------------------------------- /config/asaim-mt_tools.yaml: -------------------------------------------------------------------------------- 1 | install_tool_dependencies: True 2 | install_repository_dependencies: True 3 | install_resolver_dependencies: True 4 | 5 | tools: 6 | - name: fastqc 7 | owner: devteam 8 | revisions: 9 | - e7b2202befea 10 | tool_panel_section_label: Tools from workflows 11 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 12 | - name: cutadapt 13 | owner: lparsons 14 | revisions: 15 | - 49370cb85f0f 16 | tool_panel_section_label: Tools from workflows 17 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 18 | - name: sortmerna 19 | owner: rnateam 20 | revisions: 21 | - eb35257d2e29 22 | tool_panel_section_label: Tools from workflows 23 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 24 | - name: fastq_paired_end_interlacer 25 | owner: devteam 26 | revisions: 27 | - 3e396e702cea 28 | tool_panel_section_label: Tools from workflows 29 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 30 | - name: multiqc 31 | owner: iuc 32 | revisions: 33 | - b2f1f75d49c4 34 | tool_panel_section_label: Tools from workflows 35 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 36 | - name: metaphlan2 37 | owner: iuc 38 | revisions: 39 | - 8c82c4d90cc6 40 | tool_panel_section_label: Tools from workflows 41 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 42 | - name: humann2 43 | owner: iuc 44 | revisions: 45 | - b168c0ef3c14 46 | tool_panel_section_label: Tools from workflows 47 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 48 | - name: metaphlan2krona 49 | owner: iuc 50 | revisions: 51 | - fdbd63e92b01 52 | tool_panel_section_label: Tools from workflows 53 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 54 | - name: export2graphlan 55 | owner: iuc 56 | revisions: 57 | - ed1becc01910 58 | tool_panel_section_label: Tools from workflows 59 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 60 | - name: format_metaphlan2_output 61 | owner: bebatut 62 | revisions: 63 | - 2bfa9b200600 64 | tool_panel_section_label: Tools from workflows 65 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 66 | - name: humann2_renorm_table 67 | owner: iuc 68 | revisions: 69 | - d77397f09da1 70 | tool_panel_section_label: Tools from workflows 71 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 72 | - name: group_humann2_uniref_abundances_to_go 73 | owner: bebatut 74 | revisions: 75 | - fd2cf7c9d3ec 76 | tool_panel_section_label: Tools from workflows 77 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 78 | - name: taxonomy_krona_chart 79 | owner: crs4 80 | revisions: 81 | - c9f8fef1df74 82 | tool_panel_section_label: Tools from workflows 83 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 84 | - name: graphlan_annotate 85 | owner: iuc 86 | revisions: 87 | - 5d6f8f0bef7c 88 | tool_panel_section_label: Tools from workflows 89 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 90 | - name: humann2_genefamilies_genus_level 91 | owner: iuc 92 | revisions: 93 | - 6d364c65c946 94 | tool_panel_section_label: Tools from workflows 95 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 96 | - name: combine_metaphlan2_humann2 97 | owner: bebatut 98 | revisions: 99 | - 31394a0c0242 100 | tool_panel_section_label: Tools from workflows 101 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 102 | - name: humann2_unpack_pathways 103 | owner: iuc 104 | revisions: 105 | - 7f208f1eb64f 106 | tool_panel_section_label: Tools from workflows 107 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 108 | - name: text_processing 109 | owner: bgruening 110 | revisions: 111 | - 9ff72e942410 112 | tool_panel_section_label: Tools from workflows 113 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 114 | - name: graphlan 115 | owner: iuc 116 | revisions: 117 | - 8f62f666dcb6 118 | tool_panel_section_label: Tools from workflows 119 | tool_shed_url: https://toolshed.g2.bx.psu.edu/ 120 | -------------------------------------------------------------------------------- /config/asaim_logo.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 21 | 23 | 45 | 47 | 48 | 50 | image/svg+xml 51 | 53 | 54 | 55 | 56 | 57 | 62 | 65 | 70 | 76 | 82 | 88 | 94 | 100 | 101 | 102 | 103 | -------------------------------------------------------------------------------- /config/asaim_tools_1.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | api_key: admin 4 | galaxy_instance: http://localhost:8080 5 | install_resolver_dependencies: true 6 | install_tool_dependencies: false 7 | tools: 8 | 9 | # amplicon_sequence_processing 10 | - name: 'suite_mothur' 11 | owner: 'iuc' 12 | tool_panel_section_id: 'amplicon_sequence_processing' 13 | install_resolver_dependencies: false 14 | 15 | - name: 'suite_qiime' 16 | owner: 'iuc' 17 | tool_panel_section_id: 'amplicon_sequence_processing' 18 | install_resolver_dependencies: false 19 | 20 | - name: 'data_manager_qiime_database_downloader' 21 | owner: 'iuc' 22 | tool_panel_section_id: 'amplicon_sequence_processing' 23 | install_resolver_dependencies: false 24 | 25 | # metagenomics_manipulation 26 | - name: 'vsearch' 27 | owner: 'iuc' 28 | tool_panel_section_id: 'metagenomics_manipulation' 29 | 30 | - name: 'nonpareil' 31 | owner: 'iuc' 32 | tool_panel_section_id: 'metagenomics_manipulation' 33 | install_resolver_dependencies: false 34 | 35 | # assembly 36 | - name: 'megahit' 37 | owner: 'iuc' 38 | tool_panel_section_id: 'assembly' 39 | install_resolver_dependencies: false 40 | 41 | - name: 'metaspades' 42 | owner: 'nml' 43 | tool_panel_section_id: 'assembly' 44 | install_resolver_dependencies: false 45 | 46 | - name: 'quast' 47 | owner: 'iuc' 48 | tool_panel_section_id: 'assembly' 49 | install_resolver_dependencies: false 50 | 51 | - name: 'valet' 52 | owner: 'iuc' 53 | tool_panel_section_id: 'assembly' 54 | install_resolver_dependencies: false 55 | 56 | # wgs_taxonomic_assignations 57 | - name: 'suite_metaphlan2' 58 | owner: 'iuc' 59 | tool_panel_section_id: 'wgs_taxonomic_assignations' 60 | 61 | - name: 'format_metaphlan2_output' 62 | owner: 'bebatut' 63 | tool_panel_section_id: 'wgs_taxonomic_assignations' 64 | 65 | - name: 'suite_kraken_0_10_5' 66 | owner: 'devteam' 67 | tool_panel_section_id: 'wgs_taxonomic_assignations' 68 | install_resolver_dependencies: false 69 | -------------------------------------------------------------------------------- /config/asaim_tools_2.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | api_key: admin 4 | galaxy_instance: http://localhost:8080 5 | install_resolver_dependencies: true 6 | install_tool_dependencies: false 7 | tools: 8 | 9 | # metabolism_assignation 10 | - name: 'suite_humann2' 11 | owner: 'iuc' 12 | tool_panel_section_id: 'metabolism_assignation' 13 | 14 | - name: 'group_humann2_uniref_abundances_to_go' 15 | owner: 'bebatut' 16 | tool_panel_section_id: 'metabolism_assignation' 17 | 18 | - name: 'compare_humann2_output' 19 | owner: 'bebatut' 20 | tool_panel_section_id: 'metabolism_assignation' 21 | install_resolver_dependencies: false 22 | -------------------------------------------------------------------------------- /config/asaim_tools_3.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | api_key: admin 4 | galaxy_instance: http://localhost:8080 5 | install_resolver_dependencies: true 6 | install_tool_dependencies: false 7 | tools: 8 | 9 | # quality_control 10 | - name: 'fastqc' 11 | owner: 'devteam' 12 | tool_panel_section_id: 'quality_control' 13 | 14 | - name: 'prinseq' 15 | owner: 'iuc' 16 | tool_panel_section_id: 'quality_control' 17 | 18 | - name: 'trim_galore' 19 | owner: 'bgruening' 20 | tool_panel_section_id: 'quality_control' 21 | 22 | - name: 'trimmomatic' 23 | owner: 'pjbriggs' 24 | tool_panel_section_id: 'quality_control' 25 | 26 | - name: 'multiqc' 27 | owner: 'iuc' 28 | tool_panel_section_id: 'quality_control' 29 | 30 | # clustering 31 | - name: 'cdhit' 32 | owner: 'bebatut' 33 | tool_panel_section_id: 'clustering' 34 | install_resolver_dependencies: false 35 | 36 | - name: 'format_cd_hit_output' 37 | owner: 'bebatut' 38 | tool_panel_section_id: 'clustering' 39 | 40 | # sorting and prediction 41 | - name: 'sortmerna' 42 | owner: 'rnateam' 43 | tool_panel_section_id: 'sorting_prediction' 44 | 45 | - name: 'data_manager_sortmerna_database_downloader' 46 | owner: 'rnateam' 47 | tool_panel_section_id: 'sorting_prediction' 48 | 49 | - name: 'fraggenescan' 50 | owner: 'iuc' 51 | tool_panel_section_id: 'sorting_prediction' 52 | install_resolver_dependencies: false 53 | 54 | # similarity_search 55 | - name: 'ncbi_blast_plus' 56 | owner: 'devteam' 57 | tool_panel_section_id: 'similarity_search_alignment' 58 | install_resolver_dependencies: false 59 | 60 | - name: 'diamond' 61 | owner: 'bgruening' 62 | tool_panel_section_id: 'similarity_search_alignment' 63 | install_resolver_dependencies: false 64 | 65 | - name: 'hmmer3' 66 | owner: 'iuc' 67 | tool_panel_section_id: 'similarity_search_alignment' 68 | install_resolver_dependencies: false 69 | 70 | # mapping 71 | - name: 'bwa' 72 | owner: 'devteam' 73 | tool_panel_section_id: 'mapping' 74 | install_resolver_dependencies: false 75 | 76 | - name: 'bowtie2' 77 | owner: 'devteam' 78 | tool_panel_section_id: 'mapping' 79 | install_resolver_dependencies: false 80 | 81 | # visualization 82 | - name: 'export2graphlan' 83 | owner: 'iuc' 84 | tool_panel_section_id: 'visualization' 85 | 86 | - name: 'suite_graphlan' 87 | owner: 'iuc' 88 | tool_panel_section_id: 'visualization' 89 | 90 | - name: 'taxonomy_krona_chart' 91 | owner: 'crs4' 92 | tool_panel_section_id: 'visualization' 93 | 94 | - name: 'interproscan5' 95 | owner: 'bgruening' 96 | tool_panel_section_id: 'metabolism_assignation' 97 | install_resolver_dependencies: false 98 | 99 | - name: 'suite_picrust' 100 | owner: 'iuc' 101 | tool_panel_section_id: 'metabolism_assignation' 102 | install_resolver_dependencies: false 103 | 104 | # combination_taxo_func 105 | - name: 'combine_metaphlan2_humann2' 106 | owner: 'bebatut' 107 | tool_panel_section_id: 'combination_taxo_func' 108 | -------------------------------------------------------------------------------- /config/asaim_tools_4.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | api_key: admin 4 | galaxy_instance: http://localhost:8080 5 | install_resolver_dependencies: true 6 | install_tool_dependencies: false 7 | tools: 8 | 9 | # data_retrieval 10 | - name: 'suite_ebi_tools' 11 | owner: 'iuc' 12 | tool_panel_section_id: 'data_retrieval' 13 | 14 | - name: 'suite_enasearch' 15 | owner: 'iuc' 16 | tool_panel_section_id: 'data_retrieval' 17 | 18 | - name: 'suite_ncbi_entrez' 19 | owner: 'iuc' 20 | tool_panel_section_id: 'data_retrieval' 21 | 22 | - name: 'sra_tools' 23 | owner: 'iuc' 24 | tool_panel_section_id: 'data_retrieval' 25 | 26 | # text_manipulation 27 | - name: 'add_value' 28 | owner: 'devteam' 29 | tool_panel_section_id: 'text_manipulation' 30 | 31 | - name: 'change_case' 32 | owner: 'devteam' 33 | tool_panel_section_id: 'text_manipulation' 34 | 35 | - name: 'column_join' 36 | owner: 'jjohnson' 37 | tool_panel_section_id: 'text_manipulation' 38 | 39 | - name: 'collection_column_join' 40 | owner: 'iuc' 41 | tool_panel_section_id: 'text_manipulation' 42 | 43 | - name: 'column_maker' 44 | owner: 'devteam' 45 | tool_panel_section_id: 'text_manipulation' 46 | 47 | - name: 'concatenate_multiple_datasets' 48 | owner: 'mvdbeek' 49 | tool_panel_section_id: 'text_manipulation' 50 | 51 | - name: 'convert_characters' 52 | owner: 'devteam' 53 | tool_panel_section_id: 'text_manipulation' 54 | 55 | - name: 'cut_columns' 56 | owner: 'devteam' 57 | tool_panel_section_id: 'text_manipulation' 58 | 59 | - name: 'merge_cols' 60 | owner: 'devteam' 61 | tool_panel_section_id: 'text_manipulation' 62 | 63 | - name: 'regex_find_replace' 64 | owner: 'galaxyp' 65 | tool_panel_section_id: 'text_manipulation' 66 | 67 | - name: 'remove_beginning' 68 | owner: 'devteam' 69 | tool_panel_section_id: 'text_manipulation' 70 | 71 | - name: 'show_beginning' 72 | owner: 'devteam' 73 | tool_panel_section_id: 'text_manipulation' 74 | 75 | - name: 'show_tail' 76 | owner: 'devteam' 77 | tool_panel_section_id: 'text_manipulation' 78 | 79 | - name: 'split_file_on_column' 80 | owner: 'bgruening' 81 | tool_panel_section_id: 'text_manipulation' 82 | 83 | - name: 'unique' 84 | owner: 'bgruening' 85 | tool_panel_section_id: 'text_manipulation' 86 | 87 | - name: 'text_processing' 88 | owner: 'bgruening' 89 | tool_panel_section_id: 'text_manipulation' 90 | 91 | - name: 'suite_datamash' 92 | owner: 'iuc' 93 | tool_panel_section_id: 'text_manipulation' 94 | 95 | # seq_manipulation 96 | - name: 'seq_filter_by_id' 97 | owner: 'peterjc' 98 | tool_panel_section_id: 'seq_manipulation' 99 | install_resolver_dependencies: false 100 | 101 | - name: 'seq_rename' 102 | owner: 'peterjc' 103 | tool_panel_section_id: 'seq_manipulation' 104 | install_resolver_dependencies: false 105 | 106 | - name: 'seq_select_by_id' 107 | owner: 'peterjc' 108 | tool_panel_section_id: 'seq_manipulation' 109 | install_resolver_dependencies: false 110 | 111 | - name: 'fastq_to_fasta' 112 | owner: 'devteam' 113 | tool_panel_section_id: 'seq_manipulation' 114 | install_resolver_dependencies: false 115 | 116 | - name: 'fasta_to_tabular' 117 | owner: 'devteam' 118 | tool_panel_section_id: 'seq_manipulation' 119 | install_resolver_dependencies: false 120 | 121 | - name: 'split_paired_reads' 122 | owner: 'devteam' 123 | tool_panel_section_id: 'seq_manipulation' 124 | install_resolver_dependencies: false 125 | 126 | - name: 'fasta_add_barcode' 127 | owner: 'bebatut' 128 | tool_panel_section_id: 'seq_manipulation' 129 | install_resolver_dependencies: false 130 | 131 | - name: 'fastq_combiner' 132 | owner: 'devteam' 133 | tool_panel_section_id: 'seq_manipulation' 134 | install_resolver_dependencies: false 135 | 136 | - name: 'fastq_filter' 137 | owner: 'devteam' 138 | tool_panel_section_id: 'seq_manipulation' 139 | install_resolver_dependencies: false 140 | 141 | - name: 'fastq_groomer' 142 | owner: 'devteam' 143 | tool_panel_section_id: 'seq_manipulation' 144 | install_resolver_dependencies: false 145 | 146 | - name: 'fastq_manipulation' 147 | owner: 'devteam' 148 | tool_panel_section_id: 'seq_manipulation' 149 | install_resolver_dependencies: false 150 | 151 | - name: 'fastq_masker_by_quality' 152 | owner: 'devteam' 153 | tool_panel_section_id: 'seq_manipulation' 154 | install_resolver_dependencies: false 155 | 156 | - name: 'fastq_paired_end_deinterlacer' 157 | owner: 'devteam' 158 | tool_panel_section_id: 'seq_manipulation' 159 | install_resolver_dependencies: false 160 | 161 | - name: 'fastq_paired_end_interlacer' 162 | owner: 'devteam' 163 | tool_panel_section_id: 'seq_manipulation' 164 | install_resolver_dependencies: false 165 | 166 | - name: 'fastq_paired_end_joiner' 167 | owner: 'devteam' 168 | tool_panel_section_id: 'seq_manipulation' 169 | install_resolver_dependencies: false 170 | 171 | - name: 'fastq_paired_end_splitter' 172 | owner: 'devteam' 173 | tool_panel_section_id: 'seq_manipulation' 174 | install_resolver_dependencies: false 175 | 176 | - name: 'fastq_stats' 177 | owner: 'devteam' 178 | tool_panel_section_id: 'seq_manipulation' 179 | install_resolver_dependencies: false 180 | 181 | - name: 'fastq_to_tabular' 182 | owner: 'devteam' 183 | tool_panel_section_id: 'seq_manipulation' 184 | install_resolver_dependencies: false 185 | 186 | - name: 'fastq_trimmer' 187 | owner: 'devteam' 188 | tool_panel_section_id: 'seq_manipulation' 189 | install_resolver_dependencies: false 190 | 191 | - name: 'fastqtofasta' 192 | owner: 'devteam' 193 | tool_panel_section_id: 'seq_manipulation' 194 | install_resolver_dependencies: false 195 | 196 | - name: 'tabular_to_fastq' 197 | owner: 'devteam' 198 | tool_panel_section_id: 'seq_manipulation' 199 | install_resolver_dependencies: false 200 | 201 | - name: 'fastq_paired_end_joiner' 202 | owner: 'devteam' 203 | tool_panel_section_id: 'seq_manipulation' 204 | install_resolver_dependencies: false 205 | 206 | - name: 'fastq_join' 207 | owner: 'lparsons' 208 | tool_panel_section_id: 'seq_manipulation' 209 | install_resolver_dependencies: false 210 | 211 | # bam_sam_manipulation 212 | - name: 'suite_samtools_1_2' 213 | owner: 'devteam' 214 | tool_panel_section_id: 'bam_sam_manipulation' 215 | 216 | # biom_manipulation 217 | - name: 'suite_biom_format' 218 | owner: 'iuc' 219 | tool_panel_section_id: 'biom_manipulation' 220 | install_resolver_dependencies: false 221 | -------------------------------------------------------------------------------- /config/data_library.yaml: -------------------------------------------------------------------------------- 1 | libraries: 2 | - name: "RFAM family multiple alignment" 3 | files: 4 | - url: http://rfam.xfam.org/family/RF00005/alignment?acc=RF00005&format=stockholm&download=1 5 | file_type: stockholm 6 | #- url: http://rfam.xfam.org/family/RF01960/alignment?acc=RF01960&format=stockholm&download=1 7 | # file_type: stockholm 8 | - url: http://rfam.xfam.org/family/RF00177/alignment?acc=RF00177&format=stockholm&download=1 9 | file_type: stockholm 10 | #- url: http://rfam.xfam.org/family/RF01959/alignment?acc=RF01959&format=stockholm&download=1 11 | # file_type: stockholm 12 | -------------------------------------------------------------------------------- /config/data_managers.yaml: -------------------------------------------------------------------------------- 1 | data_managers: 2 | - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_qiime_database_downloader/data_manager_qiime_download/1.9.1 3 | # HUMAnN2 database: Protein database: full uniref50 4 | params: 5 | - 'db|database': 'greengenes' 6 | - 'db|version': '{{ item }}' 7 | items: 8 | - '13_8' 9 | data_table_reload: 10 | - qiime_rep_set 11 | - qiime_rep_set_aligned 12 | - qiime_taxonomy 13 | - qiime_trees 14 | 15 | - id: toolshed.g2.bx.psu.edu/repos/rnateam/data_manager_sortmerna_database_downloader/data_manager_sortmerna_download/2.1b.1 16 | params: 17 | - '': '{{ item }}' 18 | items: 19 | - '' 20 | data_table_reload: 21 | - rRNA_databases 22 | 23 | - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_metaphlan2_database_downloader/data_manager_metaphlan2_download/2.6.0 24 | # MetaPhlAn2 database 25 | params: 26 | - 'database': '{{ item }}' 27 | items: 28 | - db_v20 29 | data_table_reload: 30 | - metaphlan2_database 31 | 32 | - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.11.1.0 33 | # HUMAnN2 database: Nucleotide database: full chocophlan 34 | params: 35 | - 'db|database': 'chocophlan' 36 | - 'db|build': '{{ item }}' 37 | items: 38 | - full 39 | data_table_reload: 40 | - humann2_nucleotide_database 41 | 42 | - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.11.1.0 43 | # HUMAnN2 database: Protein database: full uniref50 44 | params: 45 | - 'db|database': 'uniref' 46 | - 'db|build': '{{ item }}' 47 | items: 48 | - uniref50_diamond 49 | data_table_reload: 50 | - humann2_protein_database 51 | 52 | #- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.11.1.0 53 | # # HUMAnN2 database: Protein database: full uniref90 54 | # params: 55 | # - 'db|database': 'uniref' 56 | # - 'db|build': '{{ item }}' 57 | # items: 58 | # - uniref90_diamond 59 | # data_table_reload: 60 | # - humann2_protein_database 61 | 62 | 63 | 64 | -------------------------------------------------------------------------------- /config/tool_conf.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 |