From 16a709be2cc900a552b92a4af3868a4c3f231d8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Thu, 5 Dec 2024 15:34:04 +0100 Subject: [PATCH 1/9] Create link-check.yml --- .github/workflows/link-check.yml | 71 ++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 .github/workflows/link-check.yml diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml new file mode 100644 index 000000000..32d405a20 --- /dev/null +++ b/.github/workflows/link-check.yml @@ -0,0 +1,71 @@ +name: Link Checker + +on: + repository_dispatch: + workflow_dispatch: + inputs: + logLevel: + description: 'Log level' + required: true + default: 'warning' + type: choice + options: + - info + - warning + - debug + + schedule: + - cron: "00 18 * * *" + +jobs: + linkChecker: + runs-on: ubuntu-latest + permissions: + issues: write + steps: + - uses: actions/checkout@v4 + + + - name: Setup Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: '3.1' + bundler-cache: true + cache-version: 0 + + + - name: Install dependencies + run: | + bundle install + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: | + bundle exec jekyll build + env: + PAGES_REPO_NWO: ${{ github.repository }} + JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} + JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Link Checker + id: lychee + uses: lycheeverse/lychee-action@v2 + with: + # Check all markdown, html and reStructuredText files in repo (default) + args: _site/ --fallback-extensions .html + # Don't fail action on broken links + fail: false + + - name: Add page URL + run: | + DEPLOY_URL="https://rdmkit.elixir-europe.org/" && \ + sed -i "s|\\#\\#\\# Errors in _site\/|\\#\\#\\# Errors in ${DEPLOY_URL}|g" ./lychee/out.md && \ + cat ./lychee/out.md + + - name: Create Issue From File + if: steps.lychee.outputs.exit_code != 0 + uses: peter-evans/create-issue-from-file@v5 + with: + title: Link Checker Report + content-filepath: ./lychee/out.md + labels: bug, automated issue + issue-number: 1570 From 63009700cf09ebfdb1950358e80fc9f22a6a368a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Thu, 5 Dec 2024 16:48:30 +0100 Subject: [PATCH 2/9] Update .github/workflows/link-check.yml Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> --- .github/workflows/link-check.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml index 32d405a20..3a5deebbc 100644 --- a/.github/workflows/link-check.yml +++ b/.github/workflows/link-check.yml @@ -44,6 +44,7 @@ jobs: env: PAGES_REPO_NWO: ${{ github.repository }} JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} + JEKYLL_ENV: production JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - name: Link Checker From 871c6e9997973bb25b497931a4525fb0d94a432a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Thu, 5 Dec 2024 16:49:25 +0100 Subject: [PATCH 3/9] Update link-check.yml --- .github/workflows/link-check.yml | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml index 3a5deebbc..e058101ed 100644 --- a/.github/workflows/link-check.yml +++ b/.github/workflows/link-check.yml @@ -1,19 +1,7 @@ name: Link Checker on: - repository_dispatch: workflow_dispatch: - inputs: - logLevel: - description: 'Log level' - required: true - default: 'warning' - type: choice - options: - - info - - warning - - debug - schedule: - cron: "00 18 * * *" From 12a065006d6ac553d6d684e96619bdfc12d5d737 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Thu, 5 Dec 2024 17:05:54 +0100 Subject: [PATCH 4/9] Update link-check.yml --- .github/workflows/link-check.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml index e058101ed..17a016286 100644 --- a/.github/workflows/link-check.yml +++ b/.github/workflows/link-check.yml @@ -43,6 +43,7 @@ jobs: args: _site/ --fallback-extensions .html # Don't fail action on broken links fail: false + lycheeVersion: nightly - name: Add page URL run: | From c12ca0a84c10d4e57893719794c877405273f047 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Fri, 6 Dec 2024 09:07:09 +0100 Subject: [PATCH 5/9] Update link-check.yml --- .github/workflows/link-check.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml index 17a016286..2fe5558d8 100644 --- a/.github/workflows/link-check.yml +++ b/.github/workflows/link-check.yml @@ -40,7 +40,7 @@ jobs: uses: lycheeverse/lychee-action@v2 with: # Check all markdown, html and reStructuredText files in repo (default) - args: _site/ --fallback-extensions .html + args: _site/ --fallback-extensions html # Don't fail action on broken links fail: false lycheeVersion: nightly From d9e768d94f362d62e2a8138b4f792ccc58b59cbf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Fri, 6 Dec 2024 10:39:26 +0100 Subject: [PATCH 6/9] Update link-check.yml --- .github/workflows/link-check.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/link-check.yml b/.github/workflows/link-check.yml index 2fe5558d8..6be9d7502 100644 --- a/.github/workflows/link-check.yml +++ b/.github/workflows/link-check.yml @@ -40,7 +40,7 @@ jobs: uses: lycheeverse/lychee-action@v2 with: # Check all markdown, html and reStructuredText files in repo (default) - args: _site/ --fallback-extensions html + args: _site/ --fallback-extensions html --github-token ${{ secrets.GITHUB_TOKEN }} # Don't fail action on broken links fail: false lycheeVersion: nightly From c195fdd9de8e7b53508823f889742c756d7a9885 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Fri, 6 Dec 2024 13:35:32 +0100 Subject: [PATCH 7/9] marine_metagenomics_assembly.md --- pages/tool_assembly/marine_metagenomics_assembly.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pages/tool_assembly/marine_metagenomics_assembly.md b/pages/tool_assembly/marine_metagenomics_assembly.md index d6a99ad93..539a43177 100644 --- a/pages/tool_assembly/marine_metagenomics_assembly.md +++ b/pages/tool_assembly/marine_metagenomics_assembly.md @@ -18,13 +18,13 @@ training: --- ## What is the Norwegian tool assembly for marine metagenomics data management? -The Norwegian tool assembly for marine metagenomics aims to provide a comprehensive toolkit for management of marine genomic research data throughout a project's data life cycle. The toolkit, developed by students and researchers in Norway, contains resources and software tools for both data management ([Planning](planning), [Processing](processing), [Storing](storage) and [Sharing](sharing)), data [analysis](analysing) and training. It is built on the [Norwegian e-Infrastructure for Life Sciences (NeLS)](nels_assembly) tool assembly of [ELIXIR Norway](https://elixir.no/) and the [Marine Metagenomics Platform (MMP)](https://mmp2.sfb.uit.no/). +The Norwegian tool assembly for marine metagenomics aims to provide a comprehensive toolkit for management of marine genomic research data throughout a project's data life cycle. The toolkit, developed by students and researchers in Norway, contains resources and software tools for both data management ([Planning](planning), [Processing](processing), [Storing](storage) and [Sharing](sharing)), data [analysis](analysing) and training. It is built on the [Norwegian e-Infrastructure for Life Sciences (NeLS)](nels_assembly) tool assembly of [ELIXIR Norway](https://elixir.no/) and the [Marine Metagenomics Platform (MMP)](https://sfb.mmp2.sigma2.no). ## Who can use the marine metagenomics data management tool assembly? This tool assembly is useful for students and researchers, in Norway, who are interested in analysing marine datasets (e.g. genomes, metagenomes, and transcriptomes). Parts of the assembly, such as data storage, are based on national infrastructures, laws and regulations, and consequently limited to Norwegian users, while other parts, such as data analysis tools and data repositories, are globally accessible. ## How can you access the marine metagenomics data management tool assembly? -To be able to use resources and tools that are mentioned here, you are recommended to have a [Feide account](https://www.feide.no/). In addition, it is important for you to have a NeLs account in order to access [usegalaxy.no](https://usegalaxy.no/). In case your institution does not use the national Feide secure login service, you can apply for a NeLs IDP through the [ELIXIR Norway help desk](mailto:contact@bioinfo.no?subject=marine%20metagenomics). Note, that Marine Metagenomics Platform (MMP) is an open-access platform that can be accessed without a Feide account at [https://mmp2.sfb.uit.no/](https://mmp2.sfb.uit.no/). +To be able to use resources and tools that are mentioned here, you are recommended to have a [Feide account](https://www.feide.no/). In addition, it is important for you to have a NeLs account in order to access [usegalaxy.no](https://usegalaxy.no/). In case your institution does not use the national Feide secure login service, you can apply for a NeLs IDP through the [ELIXIR Norway help desk](mailto:contact@bioinfo.no?subject=marine%20metagenomics). Note, that Marine Metagenomics Platform (MMP) is an open-access platform that can be accessed without a Feide account at [https://mmp2.sfb.uit.no/](https://sfb.mmp2.sigma2.no). ## For what purpose can you use the marine metagenomics data management tool assembly? @@ -40,7 +40,7 @@ If you use one of the National Norwegian research infrastructures, such as the N The solutions for data storage, sharing and computation are built on the services and infrastructure delivered by ELIXIR Norway described in the Norwegian e-Infrastructure for Life Sciences (NeLS) [tool assembly](nels_assembly). ### Data processing and analysis -The {% tool "marine-metagenomics-portal" %} provides a complete service for analysis of marine metagenomic data through the tool [META-pipe](https://mmp2.sfb.uit.no/metapipe/). META-pipe is a pipeline that can assemble your high-throughput sequence data, functionally annotate the predicted genes, and taxonomically profile your marine metagenomics samples, helping you to gain insight into the phylogenetic diversity, metabolic and functional potential of environmental communities. You can read more [details about META-pipe in the publication](https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC6480938/). Norwegian users with Feide access can access the online version of META-pipe. For other users META-pipe is [downloadable](https://gitlab.com/uit-sfb/metapipe) and can easily be run on any computing environment (e.g. any Linux workstation, SLURM cluster or Kubernetes). +The {% tool "marine-metagenomics-portal" %} provides a complete service for analysis of marine metagenomic data through the tool [META-pipe](https://sfb.mmp2.sigma2.no/metapipe/). META-pipe is a pipeline that can assemble your high-throughput sequence data, functionally annotate the predicted genes, and taxonomically profile your marine metagenomics samples, helping you to gain insight into the phylogenetic diversity, metabolic and functional potential of environmental communities. You can read more [details about META-pipe in the publication](https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC6480938/). Norwegian users with Feide access can access the online version of META-pipe. For other users META-pipe is [downloadable](https://gitlab.com/uit-sfb/metapipe) and can easily be run on any computing environment (e.g. any Linux workstation, SLURM cluster or Kubernetes). [Usegalaxy.no](https://usegalaxy.no/) is a Norwegian instance of the {% tool "galaxy" %} web-based platform for data intensive life science research that provides users with a unified, easy-to-use graphical interface to a host of more than 200 different analysis tools. Here, you can find tools for a wide variety of analysis for your marine metagenomic and genomic data. The tools are publicly available in the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/) which serves as an "appstore" so you can easily transfer them to your favourite Galaxy instance anywhere. You can run the tools interactively, one by one, or combine them into multi-step workflows that can be executed as a single analysis. Premade workflows (i.e for Taxonomic classification of metagenomic sequences) are provided, and you can request installation of your favourite tool by contacting the [ELIXIR Norway help desk](mailto:contact@bioinfo.no?subject=marine metagenomics). From 4b4bdbef8aac9b1d63a51eb4529a83b2967167db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Fri, 6 Dec 2024 13:36:13 +0100 Subject: [PATCH 8/9] Update no_resources.md --- pages/national_resources/no_resources.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/national_resources/no_resources.md b/pages/national_resources/no_resources.md index 9b01f2155..347aed692 100644 --- a/pages/national_resources/no_resources.md +++ b/pages/national_resources/no_resources.md @@ -49,7 +49,7 @@ national_resources: related_pages: your_tasks: [data_analysis] tool_assembly: [marine_assembly] - url: https://mmp2.sfb.uit.no/metapipe/ + url: https://sfb.mmp2.sigma2.no/metapipe/ - name: Norwegian COVID-19 Data Portal description: The Norwegian COVID-19 Data Portal aims to bundle the Norwegian research efforts and offers guidelines, tools, databases and services to support Norwegian COVID-19 researchers. related_pages: From acb3cbebbd90a40b6f7c62f23917ca11cca3eeeb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Korbinian=20B=C3=B6sl?= Date: Fri, 6 Dec 2024 13:38:40 +0100 Subject: [PATCH 9/9] tool_and_resource_list.yml --- _data/tool_and_resource_list.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index dcec6080e..ba354beda 100755 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -1252,23 +1252,23 @@ name: MarDB registry: biotools: mardb - url: https://mmp2.sfb.uit.no/mardb/ + url: https://sfb.mmp2.sigma2.no/mardb/ - description: MarFun is a manually curated marine fungi genome database. id: marfun name: MarFun - url: https://mmp2.sfb.uit.no/marfun/ + url: https://sfb.mmp2.sigma2.no/marfun/ - description: High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community id: marine-metagenomics-portal name: Marine Metagenomics Portal (MMP) registry: biotools: mmp - url: https://mmp2.sfb.uit.no/ + url: https://sfb.mmp2.sigma2.no - description: MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information id: marref name: MarRef registry: biotools: marref - url: https://mmp2.sfb.uit.no/marref/ + url: https://sfb.mmp2.sigma2.no/marref/ - description: Powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. id: mascot name: Mascot @@ -1785,7 +1785,7 @@ - description: SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae. id: saldb name: salDB - url: https://mmp.sfb.uit.no/databases/saldb/ + url: https://sfb.mmp2.sigma2.no/databases/saldb/ - description: Small Angle Scattering Biological Data Bank id: sasbdb name: SASBDB