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Merge pull request #4 from griffithlab/switch_template
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Use main template instead of website one.
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tmooney authored Aug 10, 2023
2 parents 1ec583c + 7b83978 commit 559414e
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Showing 32 changed files with 1,900 additions and 1,354 deletions.
122 changes: 97 additions & 25 deletions .github/sync.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,32 +11,104 @@ group:
test-send-updates.yml
starting-course.yml
release-notes.yml
- source: .github/workflows/delete-preview.yml
dest: .github/workflows/docker-test.yml
- source: .github/workflows/pull_request.yml
dest: .github/workflows/render-site.yml
- source: config_automation.yml
dest: config_automation.yml
docker-test.yml
docker-build.yml
- source: scripts/
dest: scripts/
deleteOrphaned: true
- source: .github/ISSUE_TEMPLATE/course-problem-report.md
dest: .github/ISSUE_TEMPLATE/course-problem-report.md
- source: .github/ISSUE_TEMPLATE/course-content-add.md
dest: .github/ISSUE_TEMPLATE/course-content-add.md
- source: style-sets
dest: style-sets
- source: assets/box_images/
dest: assets/box_images/
# Repositories to receive changes
repos: |
jhudsl/ottr-website
jhudsl/Baltimore_Community_Course
maculatus/test-ottr-website
dr-sayyadhury/OTTR_Template_Website_repo
whalera1901/Current-projects
GenetcXBiotech1/Dr.Fierst_lab
buriedsand/glbio-personal-website
PurplFeesh/test-ottr-site
jcha40/ottr_test_site
jhudsl/Documentation_and_Usability
jhudsl/Informatics_Research_Leadership
jhudsl/Data_Management_for_Cancer_Research
jhudsl/Computing_for_Cancer_Informatics
jhudsl/Adv_Reproducibility_in_Cancer_Informatics
jhudsl/Reproducibility_in_Cancer_Informatics
jhudsl/Dissemination_and_Engagement
jhudsl/Cancer_Clinical_Informatics
jhudsl/Machine_Learning_for_Cancer_Informatics
jhudsl/Cancer_Informatics_Data_Visualization
jhudsl/Cancer_Genome_Informatics
jhudsl/Cancer-Imaging-Informatics
datatrail-jhu/DataTrail_Template
abyzovlab/CNVpytor-course
opencasestudies/OCS_Guide
tmm211/dsp-terra-mooc-test2
fhdsl/Choosing_Genomics_Tools
fhdsl/NIH_Data_Sharing
fhdsl/FH_Cluster_Guide
fhdsl/Using_Leanpub
fhdsl/Ethical_Data_Handling_for_Cancer_Research
fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles
fhdsl/Design_of_Data_Analysis
fhdsl/Tools_for_Reproducible_Workflows_in_R
fhdsl/Introduction_to_reproducible_research
mccoy-lab/hgv_modules
griffithlab/pVACtools_Intro_Course
griffithlab/CIVIC_SVI_Course
PracticalGenomics/cogaps-on-sciserver
fhdsl/AI_for_software
griffithlab/Immuno_Workflow_Course
###ADD NEW REPO HERE following the format above#

### These are custom groups for syncing -- not all files needs to be synced # will update later
# - files:
# - source: config_automation.yml
# dest: config_automation.yml
# - source: .github/workflows/pull-request.yml
# dest: .github/workflows/pull-request.yml
# - source: scripts/spell-check.R
# dest: scripts/spell-check.R
# repos: |
# jhudsl/Baltimore_Community_Course
### These are custom groups for syncing -- not all files needs to be synced
- files:
- source: config_automation.yml
dest: config_automation.yml
- source: .github/workflows/pull-request.yml
dest: .github/workflows/pull-request.yml
repos: |
jhudsl/OTTR_Template_Website
- files:
- source: config_automation.yml
dest: config_automation.yml
- source: .github/workflows/delete-preview.yml
dest: .github/workflows/delete-preview.yml
- source: .github/workflows/send-updates.yml
dest: .github/workflows/send-updates.yml
- source: .github/workflows/test-send-updates.yml
dest: .github/workflows/test-send-updates.yml
- source: scripts/make_screenshots.R
dest: scripts/make_screenshots.R
- source: scripts/switch_sync_repo.R
dest: scripts/switch_sync_repo.R
repos: |
jhudsl/OTTR_Quizzes
- files:
- source: .github/workflows/
dest: .github/workflows/
exclude: |
starting-course.yml
release-notes.yml
- source: .github/switch_sync_repo.R
dest: .github/switch_sync_repo.R
- source: .github/ISSUE_TEMPLATE/course-problem-report.md
dest: .github/ISSUE_TEMPLATE/course-problem-report.md
- source: .github/ISSUE_TEMPLATE/course-content-add.md
dest: .github/ISSUE_TEMPLATE/course-content-add.md
- source: code_of_conduct.md
dest: code_of_conduct.md
- source: assets/box_images/
dest: assets/box_images/
- source: assets/style.css
dest: assets/style.css
- source: assets/toc_close.css
dest: assets/toc_close.css
- source: scripts/
dest: scripts/
deleteOrphaned: true
- source: style-sets/fhdasl/
dest: style-sets/fhdasl/
repos: |
jhudsl/AnVIL_Template
79 changes: 79 additions & 0 deletions .github/workflows/docker-build.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,79 @@
# Candace Savonen Apr 2021

name: Build Docker

on:
workflow_dispatch:
inputs:
dockerhubpush:
description: 'Push to Dockerhub?'
required: true
default: 'false'
tag:
description: 'What tag to use?'
required: true
default: 'none'
jobs:
build-docker:
name: Build Docker image
runs-on: ubuntu-latest

steps:
- name: checkout repo
uses: actions/checkout@v3

- name: Login as jhudsl-robot
run: |
git config --system --add safe.directory "$GITHUB_WORKSPACE"
git config --local user.email "[email protected]"
git config --local user.name "jhudsl-robot"
- name: Don't re-test if this is a sync branch
run: |
echo This was tested on OTTR_Template no need to re-run
# Set up Docker build
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v1

# Setup layer cache
- name: Cache Docker layers
uses: actions/cache@v2
with:
path: /tmp/.buildx-cache
key: ${{ runner.os }}-buildx-${{ github.sha }}
restore-keys: |
${{ runner.os }}-buildx-
# Set up Docker build
- name: Set up Docker Build
if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
uses: docker/setup-buildx-action@v1

- name: Get token
run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt

# Build docker image
- name: Build Docker image
uses: docker/build-push-action@v2
with:
push: false
load: true
context: docker
file: docker/Dockerfile
tags: jhudsl/base_ottr

# Login to Dockerhub
- name: Login to DockerHub
if: ${{ github.event.inputs.dockerhubpush != 'false' }}
uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}

# Push the Docker image if set to true from a manual trigger
- name: Push Docker image if manual trigger set to true
if: ${{ github.event.inputs.dockerhubpush != 'false' }}
run: |
docker tag jhudsl/base_ottr:latest jhudsl/base_ottr:$github.event.inputs.tag
docker push jhudsl/base_ottr:$github.event.inputs.tag
1 change: 1 addition & 0 deletions .github/workflows/docker-test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ jobs:
- name: Login as jhudsl-robot
run: |
git config --system --add safe.directory "$GITHUB_WORKSPACE"
git config --local user.email "[email protected]"
git config --local user.name "jhudsl-robot"
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