diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 3349cc0..87bb8ca 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -31,8 +31,9 @@ jobs: # Make the branch fresh - name: Make the branch fresh run: | - git config --local user.email "itcrtrainingnetwork@gmail.com" - git config --local user.name "jhudsl-robot" + git config --global --add safe.directory $GITHUB_WORKSPACE + git config --global user.email "itcrtrainingnetwork@gmail.com" + git config --global user.name "jhudsl-robot" branch_name='preview-${{ github.event.pull_request.number }}' echo branch doesnt exist @@ -124,9 +125,9 @@ jobs: # Set up git checkout - name: Set up git checkout run: | - git config --system --add safe.directory "$GITHUB_WORKSPACE" - git config --local user.email "itcrtrainingnetwork@gmail.com" - git config --local user.name "jhudsl-robot" + git config --global --add safe.directory $GITHUB_WORKSPACE + git config --global user.email "itcrtrainingnetwork@gmail.com" + git config --global user.name "jhudsl-robot" branch_name='preview-${{ github.event.pull_request.number }}' git fetch --all diff --git a/02-research_team.Rmd b/02-research_team.Rmd index b3942e3..a2193f7 100644 --- a/02-research_team.Rmd +++ b/02-research_team.Rmd @@ -14,17 +14,17 @@ Soil sampling for this project was done by both faculty and student volunteers f - **Fresno, CA**: Clovis Community College - **Greensboro, NC**: North Carolina A&T State University - **Harrisonburg, VA**: James Madison University -- **Honolulu, Hawai'i**: University of Hawai'i at Mānoa -- **Las Cruces, NM**: Doña Ana Community College +- **Honolulu, Hawai'i**: University of Hawai'i at Mānoa +- **Las Cruces, NM**: Doña Ana Community College - **Montgomery County, MD**: Montgomery College, Towson University - **Nashville, TN**: Meharry Medical College -- **New York, NY**: Guttman Community COllege CUNY +- **New York, NY**: Guttman Community College CUNY - **Petersburg, VA**: Virginia State University - **Seattle, WA**: North Seattle College, Pierce College -- **Tsaile, AZ**: Diné College - +- **Tsaile, AZ**: Diné College + ## Funding - + Funding for this project has been provided by the [National Human Genome Research Institute](https://www.genome.gov/) (Contract # 75N92022P00232 awarded to Johns Hopkins University), as well as by donations from [PacBio](https://www.pacb.com/) and [CosmosID](https://www.cosmosid.com/). [Advances in Genome Biology and Technology](https://www.agbt.org/) provided funding support for several team members to attend AGBT 2024. diff --git a/GA_Script.html b/GA_Script.html index 96568c1..ae5941a 100644 --- a/GA_Script.html +++ b/GA_Script.html @@ -1,10 +1,10 @@ - - - + + + diff --git a/_bookdown.yml b/_bookdown.yml index cd18ae4..91e15a2 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,6 +1,6 @@ -book_filename: "Course_Name" +book_filename: "BioDIGS in the Classroom" chapter_name: "Chapter " -repo: https://github.com/jhudsl/AnVIL_Template/ +repo: https://github.com/jhudsl/AnVIL_BioDIGS_Book/ rmd_files: ["index.Rmd", "01-BioDIGS_project_overview.Rmd", "02-research_team.Rmd", diff --git a/_output.yml b/_output.yml index 7d6b017..df9a9f2 100644 --- a/_output.yml +++ b/_output.yml @@ -1,16 +1,16 @@ bookdown::gitbook: # When using multiple css files, the default file path will be the first one # - css: [assets/style.css, assets/AnVIL_style/anvil.css] + css: [assets/style.css, assets/GDSCN_style/gdscn.css] includes: in_header: GA_Script.html - before_body: assets/AnVIL_style/big-image_anvil.html - after_body: assets/AnVIL_style/footer.html + before_body: assets/GDSCN_style/big-image_gdscn.html + after_body: assets/GDSCN_style/footer.html highlight: tango config: toc: collapse: section before: | - + after: |

This content was published with bookdown by:

The Fred Hutch Data Science Lab

diff --git a/config_automation.yml b/config_automation.yml index d90fb38..431f749 100644 --- a/config_automation.yml +++ b/config_automation.yml @@ -7,7 +7,7 @@ url-checker: yes # Render preview of content with changes (Rmd's and md's are checked) render-preview: yes # Spell check Rmds and quizzes -spell-check: no +spell-check: yes # Style any R code style-code: yes # Test build the docker image if any docker-relevant files have been changed @@ -16,11 +16,11 @@ docker-test: no ##### Renderings run upon merge to main branch ##### # Rendering each platform's content render-bookdown: yes -render-leanpub: yes -render-coursera: yes +render-leanpub: no +render-coursera: no ##### Rendering of student guide (if applicable) -render-student-guide: yes +render-student-guide: no # What docker image should be used for rendering? # The default is jhudsl/course_template:main diff --git a/index.Rmd b/index.Rmd index 151dc35..1720606 100644 --- a/index.Rmd +++ b/index.Rmd @@ -17,6 +17,7 @@ This is a companion training guide for BioDIGS, a GDSCN project that brings a re The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home). +![BioDIGS logo](https://raw.githubusercontent.com/fhdsl/AnVIL_BioDIGS_Book/main/assets/GDSCN_style/logo_BioDIGS_final.png){width=300px} ## Target Audience diff --git a/resources/dictionary.txt b/resources/dictionary.txt index 5f73e70..46de07a 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -1,26 +1,31 @@ abiotic +AGBT al Annandale AnVIL +BiocManager BioDIGS BioDiversity -BiocManager bioinformatics BIPOC Bloomberg +Brevik Buffalari callout Callout Canner +cbe colData CosmosID CoV +Cruces +culturable CUNY customizations dex dexamethasone -Din -Doa +Dine +doi dropdown El et @@ -29,23 +34,33 @@ github Glimma glimmaMDS Gmail +Gorovtsov Guttman Harrisonburg Hawai'i HBCUs +https +Illumina impactful Inclusivity +jenvman Jupyter +Jurkowski limma -MDS Manoa +MDS Meharry mentorship metagenomics Metagenomics +Nanopore +ncbi NCI NHGRI NHGRI's +nih +nlm +noa Notre Onboarding OTTR @@ -54,14 +69,19 @@ PacBio Paso Petersburg plotMDS +pmc +PMC precompiled premade preprint programmatically +pubmed px reproducibility Rmd RStudio +scitable +scitotenv Spelman timeframe Towson @@ -69,6 +89,8 @@ Tsaile underresourced underserved wip -Workspaces Workspace's +Workspaces www +Yan +