Merge pull request #9 from fhdsl/ava/themeing

Ava/themeing

.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 "[email protected]"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "[email protected]"
+          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 "[email protected]"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "[email protected]"
+          git config --global user.name "jhudsl-robot"
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all

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.

GA_Script.html

@@ -1,10 +1,10 @@
-  
-<!-- Global site tag (gtag.js) - Google Analytics -->
-<script async src="https://www.googletagmanager.com/gtag/js?id={MeasurementID}"></script>
+
+<!-- Google tag (gtag.js) -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=G-Y0D3RZ5ZHX"></script>
 <script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
 
-  gtag('config', '{MeasurementID}');
+  gtag('config', 'G-Y0D3RZ5ZHX');
 </script>

_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",

_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: |
-       <a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
+       <a href="https://www.gdscn.org/" target="_blank"><img src="assets/GDSCN_style/logo-gdscn.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
       after: |
        <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
        <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>

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

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
 

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�
-Do�a
+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
@@ -54,21 +69,28 @@ PacBio
 Paso
 Petersburg
 plotMDS
+pmc
+PMC
 precompiled
 premade
 preprint
 programmatically
+pubmed
 px
 reproducibility
 Rmd
 RStudio
+scitable
+scitotenv
 Spelman
 timeframe
 Towson
 Tsaile
 underresourced
 underserved
 wip
-Workspaces
 Workspace's
+Workspaces
 www
+Yan
+