diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index dc44201ca5b23e..b3745db8ee9e28 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,9 +1,13 @@ -!!! DELETE THIS BEFORE SUBMITTING!!! It's just a checklist to help you :) +TODO: Describe your changes here.. -1. Give your pull request a **good title** - - e.g. "Fix typo in ansible-galaxy tutorial" or "Add new transcriptomics tutorial covering a new sequencing technology" -2. Describe your changes in detail, list anything you still need some help with or things that are still TODO -3. Check that your images are allowed to be re-hosted by the GTN! -4. Not ready for review yet? Make it a **Draft** pull request + diff --git a/.github/workflows/ci-main.yml b/.github/workflows/ci-main.yml index a4b9adb8e97708..21993c3c2934a1 100644 --- a/.github/workflows/ci-main.yml +++ b/.github/workflows/ci-main.yml @@ -17,7 +17,7 @@ on: - 'news/**' - 'events/**' - CONTRIBUTORS.yaml - - FUNDERS.yaml + - GRANTS.yaml - ORGANISATIONS.yaml @@ -66,8 +66,8 @@ jobs: - name: Check Tutorial Formatting run: | - find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review - bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-on-error + find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review -fail-level=any + bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-level=any env: REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 96cc207e8f5421..a626f68365b535 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -51,11 +51,12 @@ jobs: ${{ runner.os }}-gems- - name: Install dependencies run: | - sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node + sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config graphviz # for node gem install bundler bundle config path vendor/bundle bundle install --jobs 4 --retry 3 - npm install + rm -f package.json package-lock.json yarn.lock + npm install markdown-yaml-metadata-parser lunr bundle pristine ffi # END Dependencies @@ -68,7 +69,6 @@ jobs: make annotate ACTIVATE_ENV=pwd curl -L https://docs.google.com/spreadsheets/d/1NfZhi5Jav7kl9zFCkeb7rIC2F8xW1isruv1TeO4WpNI/export\?format\=tsv | ruby bin/prepare_feedback.rb curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json - npm install make rebuild-search-index ACTIVATE_ENV=pwd cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json rdoc bin _plugins/ --output gtn_rdoc diff --git a/.github/workflows/monthly-release-backfill.yml b/.github/workflows/monthly-release-backfill.yml index b8171611e85e6f..af77c5010ca076 100644 --- a/.github/workflows/monthly-release-backfill.yml +++ b/.github/workflows/monthly-release-backfill.yml @@ -47,7 +47,8 @@ jobs: pip install pyyaml bundle config path vendor/bundle bundle install --jobs 4 --retry 3 - npm install + rm -f package.json package-lock.json yarn.lock + npm install markdown-yaml-metadata-parser lunr bundle pristine ffi # END Dependencies @@ -68,7 +69,6 @@ jobs: sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json - npm install make rebuild-search-index ACTIVATE_ENV=pwd cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material diff --git a/.github/workflows/monthly-release.yml b/.github/workflows/monthly-release.yml index 8af9d9e70c7280..95fec41a22a680 100644 --- a/.github/workflows/monthly-release.yml +++ b/.github/workflows/monthly-release.yml @@ -54,7 +54,8 @@ jobs: pip install pyyaml bundle config path vendor/bundle bundle install --jobs 4 --retry 3 - npm install + rm -f package.json package-lock.json yarn.lock + npm install markdown-yaml-metadata-parser lunr bundle pristine ffi # END Dependencies @@ -70,7 +71,6 @@ jobs: sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json - npm install make rebuild-search-index ACTIVATE_ENV=pwd cat metadata/swagger.yaml | ruby bin/yaml2json.rb > api/swagger.json JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material diff --git a/.github/workflows/social.yml b/.github/workflows/social.yml new file mode 100644 index 00000000000000..bca03c1472031d --- /dev/null +++ b/.github/workflows/social.yml @@ -0,0 +1,75 @@ +name: "[Social] Autogenerate missing social media cards" + +on: + schedule: + # * is a special character in YAML so you have to quote this string + # We'll run this weekly at noon. + - cron: '0 12 * * 0' + workflow_dispatch: + inputs: + all_old: + type: string + description: If you want to re-generate ALL images set to a non-empty value + +jobs: + runner-job: + if: github.repository_owner == 'galaxyproject' + runs-on: ubuntu-latest + steps: + # Shallow should be fine for video + - uses: actions/checkout@v4 + with: + fetch-depth: 500 + + # BEGIN Dependencies + - uses: actions/setup-python@v5 + with: + python-version: '3.11' + architecture: 'x64' + - name: Install dependencies + run: | + sudo apt-get install -y imagemagick + pip install requests + mkdir -p ~/.fonts/ + wget https://galaxy-training.s3.amazonaws.com/social/recursive.ttf -O ~/.fonts/recursive.ttf + fc-cache -rv + # END Dependencies + + + # We get the previous build ID to know how many videos were changed since + # then. + # + # We *could* fetch the diff in the past N days but if a build fails for + # any reason, we'd lose those changes permanently and things would never + # get built. + # + # So instead we just track the last successfully built timestamp + - name: Previous build ID + id: build_id + run: | + echo "timestamp=$(curl https://galaxy-training.s3.amazonaws.com/social/timestamp.txt -f 2>/dev/null || echo none)" >> $GITHUB_ENV + + # Support regenerating all + if [[ "${{ github.event.inputs.selected_tag }}" != "" ]]; then + echo "timestamp=0" >> $GITHUB_ENV + fi + + # The actual compilation process deposits everything in the ./social/ folder. + # And requires fetching metadata from the live website (api/social-meta.json) + - name: Build Social Media Cards + run: | + mkdir -p social/ + python bin/social-cards.py $PREVIOUS_TIMESTAMP + env: + PREVIOUS_TIMESTAMP: ${{ env.timestamp }} + + # Deploy step, scary. + - uses: jakejarvis/s3-sync-action@v0.5.1 + with: + args: --acl public-read --follow-symlinks + env: + AWS_S3_BUCKET: galaxy-training + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + SOURCE_DIR: './social/' + DEST_DIR: 'social/' diff --git a/.github/workflows/video.yml b/.github/workflows/video.yml index 30aa5d693d5b73..0ec03340f8a73a 100644 --- a/.github/workflows/video.yml +++ b/.github/workflows/video.yml @@ -10,7 +10,7 @@ on: jobs: runner-job: if: github.repository_owner == 'galaxyproject' - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 services: # Label used to access the service container mozillatts: diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index 8295dfe2473598..3edfdf18851df1 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -331,6 +331,10 @@ bernt-matthias: joined: 2017-09 elixir_node: de +bethanmanley: + name: Bethan Manley + joined: 2024-09 + bethlehem-adnew: name: Bethlehem Adnew joined: 2024-06 @@ -701,7 +705,7 @@ angiolini: joined: 2024-05 elixir_node: uk orcid: 0000-0002-0814-8830 - + emmaleith: name: Emma Leith email: leith023@umn.edu @@ -836,7 +840,7 @@ GabrielaLopez: orcid: 0000-0002-0814-8830 joined: 2023-01 elixir_node: uk - + gallardoalba: name: Cristóbal Gallardo joined: 2020-11 @@ -906,6 +910,7 @@ hechth: joined: 2020-01 email: helge.hecht@recetox.muni.cz orcid: 0000-0001-6744-996X + elixir_node: cz heylf: name: Florian Heyl @@ -945,6 +950,13 @@ hexylena: lat: 51.91 lon: 4.46 +hfraser: + name: Heather Fraser + joined: 2024-09 + email: heather.fraser@open.ac.uk + elixir_node: uk + github: false + hmenager: name: Hervé Ménager joined: 2017-09 @@ -993,7 +1005,7 @@ hujambo-dunia: igcbioinformatics: name: IGC Bioinformatics Unit joined: 2018-12 - + igormakunin: name: Igor Makunin joined: 2024-09 @@ -1356,7 +1368,7 @@ LonsBio: loraine-gueguen: name: Loraine Guéguen joined: 2017-09 - + lybCNU: name: Yongbin Li joined: 2024-08 @@ -1546,7 +1558,7 @@ Melkeb: melpetera: name: Mélanie Petera joined: 2019-06 - + meltemktn: name: Meltem Kutnu joined: 2024-09 @@ -1557,6 +1569,12 @@ mgramm1: orcid: 0000-0002-4217-5277 joined: 2021-03 +mhintze: + name: Mark Hintze + email: mark.hintze@open.ac.uk + joined: 2024-09 + github: false + miaomiaozhou88: name: Miaomiao Zhou email: m.zhou1@avans.nl @@ -1669,7 +1687,7 @@ nakucher: name: Natalie Kucher email: nkucher3@jhu.edu joined: 2023-06 - + natalie-wa: name: Natalie Whitaker-Allen email: nwhitak5@jh.edu @@ -1822,6 +1840,19 @@ RareSeas: name: Adelaide Rhodes joined: 2021-05 +paige-kulzer: + name: Paige Kulzer + joined: 2024-10 + email: pkulzer@charlotte.edu + linkedin: paige-kulzer-210b97274 + contact_for_training: true + bio: + "My current role involves bioinformatics, data management, and training for a genome browser called the Integrated Genome Browser (IGB)." + location: + country: US + lat: 35.227 + lon: -80.843 + PatCapon39: name: Patrick Capon joined: 2024-02 @@ -1866,7 +1897,7 @@ paulzierep: pavanvidem: name: Pavankumar Videm - orcid: 0000-0002-5192-126X + orcid: 0000-0002-5192-126X joined: 2017-09 affiliations: - uni-freiburg @@ -2132,7 +2163,7 @@ shwdey: name: Shweta Pandey email: shwphd@gmail.com joined: 2024-06 - + simonbray: name: Simon Bray joined: 2019-05 @@ -2175,6 +2206,11 @@ slugger70: "Have I told you about my watch?" +SNG888: + name: Sandra Ng + email: s.ng@qmul.ac.uk + joined: 2023-07 + Sofokli5: name: Sofoklis Keisaris email: sofoskeisaris@gmail.com @@ -2229,6 +2265,10 @@ suchitrathapa: name: Suchitra Thapa joined: 2021-11 +sujaikumar: + name: Sujai Kumar + joined: 2024-09 + supernord: name: Johan Gustafsson joined: 2024-02 @@ -2251,6 +2291,12 @@ tb143: name: Tim Beck joined: 2023-09 +tbrown91: + name: Tom Brown + email: brown@izw-berlin.de + orcid: 0000-0001-8293-4816 + joined: 2024-08 + tcollins2011: name: Tyler Collins joined: 2024-09 @@ -2281,6 +2327,16 @@ themudo: name: Gonçalo Themudo joined: 2021-10 +ThibaudGlinez: + name: Glinez Thibaud + email: thibaud.glinez@mnhn.fr + orcid: 0009-0006-8655-7505 + joined: 2024-02 + elixir_node: fr + affiliations: + - pndb + - elixir-europe + thobalose: name: Thoba Lose joined: 2019-11 @@ -2301,7 +2357,7 @@ timonschlegel: name: Timon Schlegel orcid: 0009-0001-3228-105X joined: 2024-05 - + timothygriffin: name: Timothy J. Griffin email: tgriffin@umn.edu @@ -2356,7 +2412,7 @@ tsenapathi: trungN: name: Nguyen Vo Minh Trung - joined: 2024-09 + joined: 2024-09 TKlingstrom: name: Tomas Klingström @@ -2411,6 +2467,8 @@ wee-snufkin: name: Julia Jakiela email: juliajot36@gmail.com joined: 2022-06 + elixir_node: uk + orcid: 0009-0001-2017-8805 willdurand: name: William Durand @@ -2440,6 +2498,12 @@ wm75: - uni-freiburg - elixir-europe +wverastegui: + name: Wudmir Rojas + email: wudmir.rojas@recetox.muni.cz + joined: 2024-10 + elixir_node: cz + xiliu: name: Xi Liu github: false @@ -2493,6 +2557,11 @@ yvesvdb: affiliations: - ifb +zargham-ahmad: + name: Zargham Ahmad + email: zargham.ahmad@recetox.muni.cz + joined: 2024-10 + elixir_node: cz SNG888: name: Sandra Ng diff --git a/FUNDERS.yaml b/GRANTS.yaml similarity index 72% rename from FUNDERS.yaml rename to GRANTS.yaml index a39b2e6a50ca77..4d1d3eb67a5ec4 100644 --- a/FUNDERS.yaml +++ b/GRANTS.yaml @@ -1,33 +1,27 @@ -# List of funders related to contributors +--- +# List of grants funding GTN contributions # -# reference funders by their id in tutorial metadata files +# Grants can be listed as affiliations for contributors +# Grants can be listed as funding contributors on training materials # # valid tags: -# name, email, linkedin, twitter, gitter, orcid, bio, joined, url, -# funder, funding_id, funding_system, funding_statement +# name, joined, url, github, funding_id, funding_database, funding_statement # -# collection names should be equal to github username, if not, add github: false tag ---- - -# funder1: -# name: Funder A +# EXAMPLE +# +# Grant1: # should be equal to GitHub username if one exists for the grant/project +# name: Grant/Project name +# github: false # add this if the id does not map to a GitHub account # joined: 2020-06 -# url: "https://example.com" -# funder: true -# funding_id: 2020-1-NL01-KA203-064717 -# funding_system: erasmusplus -# funding_statement: "This project is funded with the support of .." +# url: "https://example.com" # homepage of the project +# funding_statement: "This project is funded with the support of .." # optional, if you want a specific bit of text to appear +# funding_id: 2020-1-NL01-KA203-064717 # id of your grant, will be used in combination with funding_database to link to offical grant page +# funding_database: cordis|highergov|ukri|erasmusplus # Database where your project/grant is listed, +# # EU grants are often listed in cordis, US grants in highergov, UK grants in ukri +# # If your project is not present in one of these databases, please ping us. +# +# Please add in alphabetical order of the key (id) -# our real funders <3 -# please add in alphabetical order of the key (id) - -abromics: - name: ABRomics - github: false - joined: 2024-01 - avatar: "/training-material/assets/images/abromics.png" - url: https://www.abromics.fr/ - funder: true ai4life: name: AI4Life @@ -35,9 +29,8 @@ ai4life: joined: 2023-07 avatar: "/training-material/topics/ai4life/images/AI4Life-logo_giraffe-solid.png" url: https://ai4life.eurobioimaging.eu/ - funder: true funding_id: "101057970" - funding_system: cordis + funding_database: cordis funding_statement: | AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. @@ -47,18 +40,16 @@ biont: joined: 2023-09 avatar: "/training-material/assets/images/BioNT_Logo.png" url: https://biont-training.eu/ - funder: true funding_id: "101100604" - funding_system: cordis + funding_database: cordis funding_statement: | Co-funded by the European Union by-covid: name: BeYond-COVID joined: 2023-04 - funder: true funding_id: "101046203" - funding_system: cordis + funding_database: cordis funding_statement: | BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. @@ -70,23 +61,11 @@ CINECA-Project: name: Common Infrastructure for National Cohorts in Europe, Canada, and Africa short_name: "CINECA" joined: 2023-03 - funder: true funding_id: "825775" - funding_system: cordis + funding_database: cordis funder_name: Horizon 2020 url: https://www.cineca-project.eu -nfdi4plants: - name: DataPLANT - joined: 2024-07 - url: https://www.nfdi4plants.de://www.nfdi4plants.de/ - avatar: "/training-material/shared/images/logo-dataplant.svg" - funder: true - -deNBI: - name: de.NBI - funder: true - url: https://www.denbi.de/ elixir-converge: name: ELIXIR-CONVERGE @@ -94,9 +73,8 @@ elixir-converge: joined: 2023-01 avatar: "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png" url: https://elixir-europe.org/about-us/how-funded/eu-projects/converge - funder: true funding_id: "871075" - funding_system: cordis + funding_database: cordis funding_statement: | ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement № 871075 @@ -107,25 +85,19 @@ edctp-eu: avatar: "/training-material/shared/images/edctp-eu.png" github: false url: https://www.edctp.org/ - funder: true + funding_id: "101103640" + funding_database: cordis funding_statement: | TB-CAPT, PanACEA and PANGenS are part of the EDCTP2 and EDCTP3 programs supported by the European Union. -elixir-excelerate: - name: Elixir Excelerate - url: https://www.elixir-europe.org/excelerate/ - avatar: "/training-material/shared/images/Excelerate_whitebackground.png" - github: false - funder: true elixir-fair-data: name: "ELIXIR-UK: FAIR Data Stewardship training" short_name: "ELIXIR Fair Data" github: false joined: 2023-06 - funder: true funding_id: MR/V038966/1 - funding_system: ukri + funding_database: ukri funding_statement: | This work has been funded by the ELIXIR-UK FAIR Data Stewardship training UKRI award (MR/V038966/1) @@ -136,8 +108,7 @@ elixir-uk-dash: github: false avatar: "/training-material/shared/images/dash.png" url: https://elixiruknode.org/projects/elixir-uk-dash/ - funder: true - funding_system: ukri + funding_database: ukri funding_id: MR/V038966/1 funding_statement: | This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources. @@ -147,9 +118,8 @@ eosc-life: github: false joined: 2023-04 avatar: "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png" - funder: true funding_id: "824087" - funding_system: cordis + funding_database: cordis funding_statement: | EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087 url: https://www.eosc-life.eu @@ -160,19 +130,20 @@ epsrc-training-grant: short_name: "EPSRC/OU" github: false joined: 2022-09 - funder: true + funding_id: "EP/T518165/1" + funding_database: ukri funding_statement: The research internship was supported through EPSRC Training Grant DTP 2020-2021 Open University url: "https://www.open.ac.uk/" + eurosciencegateway: name: EuroScienceGateway github: false joined: 2023-10 avatar: "/training-material/assets/images/eurosciencegateway.png" url: https://galaxyproject.org/projects/esg/ - funder: true funding_id: "101057388" - funding_system: cordis + funding_database: cordis funding_statement: | EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963. @@ -183,9 +154,8 @@ fairease: joined: 2023-10 avatar: "/training-material/assets/images/fair_ease_colour.png" url: https://fairease.eu/ - funder: true funding_id: "101058785" - funding_system: cordis + funding_database: cordis funding_statement: | FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe. @@ -195,7 +165,6 @@ fnso2019: joined: 2023-05 avatar: "/training-material/shared/images/fnso.png" github: false - funder: true url: "https://www.ouvrirlascience.fr/national-fund-for-open-science/" funder_name: National Fund for Open Science funding_id: AAPFNSO2019OpenMetaPaper-14026 @@ -212,11 +181,10 @@ gallantries: joined: 2020-09 avatar: "https://gallantries.github.io/assets/images/gallantries-logo.png" github: false - funder: true url: "https://www.erasmusplus.nl" funder_name: Erasmus+ Programme funding_id: 2020-1-NL01-KA203-064717 - funding_system: erasmusplus + funding_database: erasmusplus funding_statement: | This project ([`2020-1-NL01-KA203-064717`](https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717)) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics. ![eu flag with the text: with the support of the erasmus programme of the european union](https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg) @@ -228,32 +196,14 @@ h2020-defend: short_name: DEFEND github: false joined: 2023-05 - funder: true funding_id: "773701" - funding_system: cordis + funding_database: cordis funding_statement: | DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe. This work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 773701. url: https://www.defend2020.eu -madland: - name: MAdLand - joined: 2024-07 - url: https://madland.science - avatar: "/training-material/shared/images/logo-madland.jpg" - funder: true - github: false - -mwk: - name: Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg - short_name: MWK - joined: 2024-08 - url: https://mwk.baden-wuerttemberg.de/de/startseite - avatar: "/training-material/assets/images/MWK.png" - funder: true - github: false - nhgri-anvil: name: National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space short_name: "NHGRI ANVIL" @@ -261,7 +211,6 @@ nhgri-anvil: joined: 2023-06 avatar: https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png url: https://www.genome.gov/Funded-Programs-Projects/Computational-Genomics-and-Data-Science-Program/Genomic-Analysis-Visualization-Informatics-Lab-space-AnVIL - funder: true funding_id: U24HG010263 nhgri-gdscn: @@ -271,39 +220,11 @@ nhgri-gdscn: joined: 2023-06 avatar: https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png url: https://www.genome.gov/ - funder: true funding_id: 75N92022P00232 - -NIH: - name: National Institutes of Health - short_name: "NIH" - avatar: /training-material/shared/images/nih.png - url: https://nih.gov/ - funder: true - github: false + funding_database: highergov -nsf: - name: National Science Foundation - url: https://www.nsf.gov - avatar: "/training-material/shared/images/nsf.gif" - github: false - funder: true - -sfb992: - name: Collaborative Research Centre 992 - url: https://www.sfb992.uni-freiburg.de/ - avatar: https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg - github: false - funder: true -ukmrc: - name: UK Medical Research Council - url: https://mrc.ukri.org - avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/master/logo.png - github: false - funder: true - diff --git a/Gemfile.lock b/Gemfile.lock index 74f96469c95bac..417dd1e86c7e42 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -110,7 +110,7 @@ GEM typhoeus (1.4.0) ethon (>= 0.9.0) unicode-display_width (2.5.0) - webrick (1.8.1) + webrick (1.8.2) yell (2.2.2) zeitwerk (2.6.12) diff --git a/ORGANISATIONS.yaml b/ORGANISATIONS.yaml index 4817d2975d7121..7a55f6b3e7d229 100644 --- a/ORGANISATIONS.yaml +++ b/ORGANISATIONS.yaml @@ -1,13 +1,21 @@ --- -# List of contributing organisations +# List of contributing organisations and projects # -# reference maintainers/contributors by their id in tutorial metadata files +# Organisations can be listed as affiliations for contributors +# Organisations can be listed as funding contributors on training materials # # valid tags: name, email, linkedin, twitter, gitter, orcid, bio, joined # -# collection names should be equal to github username, if not, add github: false tag +# ID should be equal to github username if one exists, otherwise add 'github: false' +# +# Please add organisations in alphabetical order -# our real contributing organisations <3 (please add them in alphabetical order) +abromics: + name: ABRomics + github: false + joined: 2024-01 + avatar: "/training-material/assets/images/abromics.png" + url: https://www.abromics.fr/ AustralianBioCommons: name: Australian BioCommons @@ -15,6 +23,7 @@ AustralianBioCommons: avatar: "/training-material/shared/images/Australian-Biocommons-Favicon-RGB.png" avans-atgm: + short_name: Avans name: Avans Hogeschool joined: 2020-11 url: https://avans.nl @@ -26,6 +35,10 @@ carpentries: joined: 2021-09 ror: "0356fgm10" +deNBI: + name: de.NBI + url: https://www.denbi.de/ + earlham: name: Earlham Institute joined: 2017-09 @@ -34,8 +47,8 @@ earlham: ror: "018cxtf62" edctp: - name: EDCTP - description: The European & Developing Countries Clinical Trials Partnership + short_name: EDCTP + name: The European & Developing Countries Clinical Trials Partnership url: https://www.edctp.org/ avatar: "/training-material/shared/images/edctp.jpg" github: false @@ -48,6 +61,13 @@ egi: github: false ror: "052jj4m32" + +elixir-excelerate: + name: ELIXIR Excelerate + url: https://www.elixir-europe.org/excelerate/ + avatar: "/training-material/shared/images/Excelerate_whitebackground.png" + github: false + elixir-europe: name: ELIXIR Europe joined: 2017-09 @@ -56,28 +76,30 @@ elixir-europe: ror: "044rwnt51" elixir-goblet-ttt: + short_name: Goblet name: ELIXIR Goblet Train the Trainers joined: 2022-09 github: false avatar: "/training-material/shared/images/elixir.png" embl-ebi: - name: EMBL-EBI - description: European Bioinformatics Institute + short_name: EMBL-EBI + name: European Bioinformatics Institute url: https://www.ebi.ac.uk avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/d0fccaa9dc8dc8615eb7146d6c5e96bd36f11f3a/EMBL_EBI_Logo_black.svg github: false ror: "02catss52" erasmusmc: - name: ErasmusMC - description: Erasmus Medical Center + short_name: ErasmusMC + name: Erasmus Medical Center url: https://www.erasmusmc.nl avatar: "/training-material/shared/images/logo-erasmusmc.png" github: false ror: "018906e22" eu: + short_name: EU name: The European Union url: https://european-union.europa.eu avatar: "/training-material/shared/images/EU-logo.jpg" @@ -85,14 +107,15 @@ eu: ror: "019w4f821" find: - name: FIND - description: The Foundation for Innovative New Diagnostics + short_name: FIND + name: The Foundation for Innovative New Diagnostics url: https://www.finddx.org/ avatar: "/training-material/shared/images/FIND.png" github: false ror: "05tcsqz68" ifb: + short_name: IFB name: Institut Français de Bioinformatique url: https://www.france-bioinformatique.fr/ avatar: "/training-material/shared/images/ifb.png" @@ -106,6 +129,7 @@ inab-certh: ror: "03bndpq63" irccs: + short_name: IRCCS name: IRCCS Ospedale San Raffaele url: "https://www.hsr.it/" avatar: "/training-material/shared/images/irccs.jpg" @@ -119,6 +143,7 @@ jetstream2: github: false johnshopkins: + short_name: JHU name: Johns Hopkins University url: "https://www.jhu.edu/" avatar: "/training-material/shared/images/hopkins.png" @@ -126,13 +151,22 @@ johnshopkins: ror: "00za53h95" linq: - name: LINQ - description: LINQ management GmbH - link: "https://linq-management.com/" + short_name: LINQ + name: LINQ management GmbH + url: "https://linq-management.com/" avatar: "/training-material/shared/images/linq.jpg" github: false +madland: + short_name: MAdLand + name: "MAdLand - Molecular Adaptation to Land: plant evolution to change" + joined: 2024-07 + url: https://madland.science + avatar: "/training-material/shared/images/logo-madland.jpg" + github: false + minnesotauni: + short_name: UMN name: University of Minnesota url: "https://twin-cities.umn.edu/" avatar: "/training-material/shared/images/minnesotauni.png" @@ -140,45 +174,79 @@ minnesotauni: ror: "017zqws13" MPIIE: + short_name: MPIEE name: Max Planck Institute of Immunology and Epigenetics url: https://www.ie-freiburg.mpg.de avatar: https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif github: false ror: "058xzat49" +mwk: + name: Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg + short_name: MWK + joined: 2024-08 + url: https://mwk.baden-wuerttemberg.de/de/startseite + avatar: "/training-material/assets/images/MWK.png" + github: false + ncbi: + short_name: NCBI name: National Center for Biotechnology Information url: "https://www.ncbi.nlm.nih.gov/" avatar: "/training-material/shared/images/ncbi.png" ror: "02meqm098" +nfdi4plants: + short_name: DataPLANT + name: NFDI4Plants/DataPLANT + joined: 2024-07 + url: https://www.nfdi4plants.de://www.nfdi4plants.de/ + avatar: "/training-material/shared/images/logo-dataplant.svg" + +NIH: + name: National Institutes of Health + short_name: "NIH" + avatar: /training-material/shared/images/nih.png + url: https://nih.gov/ + github: false + +nsf: + short_name: NSF + name: National Science Foundation + url: https://www.nsf.gov + avatar: "/training-material/shared/images/nsf.gif" + github: false + panacea: - name: PanACEA - description: Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics + short_name: PanACEA + name: Pan-African Consortium for the Evaluation of Antituberculosis Antibiotics url: https://panacea-tb.net/ avatar: "/training-material/shared/images/panacea.jpg" github: false pangens: - name: PANGenS - description: Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens + short_name: PANGenS + name: Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens url: https://pangens.org/ avatar: "/training-material/shared/images/pangens.jpg" github: false petermac: + short_name: PeterMac name: Peter MacCallum Cancer Centre url: "https://www.petermac.org/" avatar: "/training-material/shared/images/petermac.png" ror: "02a8bt934" pndb: + short_name: PNDB name: Pôle National de Données de Biodiversité url: https://www.pndb.fr/ avatar: "/training-material/shared/images/PNDB_sub.png" github: false psu: + short_name: PSU name: The Pennsylvania State University url: http://www.psu.edu avatar: "/training-material/shared/images/psu.png" @@ -186,20 +254,22 @@ psu: ror: "04p491231" qiime2: + short_name: QIIME2 name: QIIME2 url: https://qiime2.org/ avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4 sanbi: - name: SANBI/UWC + short_name: SANBI/UWC url: https://www.sanbi.org/ avatar: "/training-material/shared/images/sanbi.png" - description: "South African National Bioinformatics Institute, University of the Western Cape" + name: "South African National Bioinformatics Institute, University of the Western Cape" github: false ror: "005r3tp02" san-raffaele-uni: + short_name: UniSR name: Università Vita-Salute San Raffaele url: "https://www.unisr.it/" avatar: "/training-material/shared/images/uni_san_raffaele.svg" @@ -213,7 +283,22 @@ sciensano: github: false ror: "04ejags36" +sfb992: + short_name: CRC992 + name: Collaborative Research Centre 992 + url: https://www.sfb992.uni-freiburg.de/ + avatar: https://raw.githubusercontent.com/bgruening/presentations/bce348bb606c312d531c479e63a66efc2bc38d44/shared/resources/img/MEDEP.jpg + github: false + +societyprotectionundergroundnetworks: + short_name: SPUN + name: Society for the Protection of Underground Networks + description: "SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection." + url: "https://www.spun.earth" + avatar: "/training-material/shared/images/spun-logo.png" + swiss-tph: + short_name: SwissTPH name: Swiss Tropical and Public Health Institute url: https://www.swisstph.ch/en/ avatar: "/training-material/shared/images/swiss-tph.png" @@ -221,19 +306,29 @@ swiss-tph: ror: "03adhka07" tb-capt: + short_name: TB-CAPT name: TB-CAPT url: https://www.tb-capt.org/ avatar: "/training-material/shared/images/tb_capt.svg" github: false uga: + short_name: UGA name: Université Grenoble-Alpes url: https://www.univ-grenoble-alpes.fr/ avatar: /training-material/shared/images/logo-uga.svg github: false ror: "02rx3b187" +ukmrc: + short_name: UKRI-MRC + name: UK Medical Research Council + url: https://mrc.ukri.org + avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/master/logo.png + github: false + uni-freiburg: + short_name: UFR name: University of Freiburg url: https://www.uni-freiburg.de/ avatar: https://raw.githubusercontent.com/bgruening/presentations/a2e38e4b007994af798320db3a0131c4bb891c0e/shared/resources/img/logo_freiburg.jpg @@ -241,6 +336,7 @@ uni-freiburg: ror: "0245cg223" UTas: + short_name: UTas name: University of Tasmania url: https://www.utas.edu.au/ avatar: "/training-material/shared/images/UTas_logo.png" @@ -248,6 +344,7 @@ UTas: ror: "01nfmeh72" vib: + short_name: VIB name: Vlaams Instituut voor Biotechnologie url: https://vib.be/ avatar: "/training-material/shared/images/logo-vib.png" diff --git a/_config.yml b/_config.yml index 2a57d792bd1109..51eabde7fdaae9 100644 --- a/_config.yml +++ b/_config.yml @@ -166,6 +166,7 @@ icon-tag: galaxy-toggle: fas fa-toggle-on galaxy-upload: fas fa-upload galaxy-download: fas fa-download + galaxy-wf-best-practices: fas fa-wand-magic-sparkles galaxy-wf-connection: fas fa-arrows-alt-h galaxy-wf-edit: fa fa-edit galaxy-wf-new: fas fa-plus diff --git a/_includes/funding-statement.md b/_includes/funding-statement.md index d2f72e4526ebce..47bef4df50ea78 100644 --- a/_includes/funding-statement.md +++ b/_includes/funding-statement.md @@ -3,7 +3,7 @@ {% for id in include.funders %} {% assign name = site.data.contributors[id].name | default: id -%} - {% assign pfo = site.data.funders[id] | default: site.data.organisations[id] | default: site.data.contributors[id] | default: nil %} + {% assign pfo = site.data.grants[id] | default: site.data.organisations[id] | default: site.data.contributors[id] | default: nil %}
{% if pfo.avatar %} Logo @@ -17,7 +17,7 @@
{{ pfo.short_name | default: pfo.name | default: id }}
- {{ site.data.funders[id].funding_statement | markdownify | strip_html }} + {{ site.data.grants[id].funding_statement | markdownify | strip_html }} {{ pfo.description }}
diff --git a/_includes/tutorial_list.html b/_includes/tutorial_list.html index 5d869ba99575ee..a49f8713d4e49c 100644 --- a/_includes/tutorial_list.html +++ b/_includes/tutorial_list.html @@ -44,7 +44,12 @@ {% endif %} {% if material.layout == 'custom' %} - {{material.title | markdownify }} + + {{material.title | markdownify }} + + {{material.description | markdownify }} {% else %} diff --git a/_layouts/base.html b/_layouts/base.html index c1c245d072c7e5..293930649ee22f 100644 --- a/_layouts/base.html +++ b/_layouts/base.html @@ -46,7 +46,13 @@ {%- elsif page.tags contains "gat" %}{% assign coverimage = "assets/images/gat.png" %} {%- else %}{% assign coverimage = "assets/images/GTNLogo1000.png" %}{% endif %} {% assign og_image = page.og_image | default: page['cover-image'] | default: topic.og_image | default: coverimage | default: "assets/images/GTNLogo1000.png" %} + {%- if page.layout == "tutorial_hands_on" or page.layout == "tutorial_slides" or page.layout == "event" or page.layout == "workflow" or page.layout == "faq" or page.layout == "introduction_slides" or page.layout == "learning-pathway" -%} + + {% elsif page.layout == "topic" or page.layout == "recordings" %} + + {%- else -%} + {%- endif -%} {%- if page.layout == "tutorial_hands_on" -%}