diff --git a/.github/workflows/biol1435-spring-tag.yml b/.github/workflows/biol1435-spring-tag.yml new file mode 100644 index 0000000..d6922b0 --- /dev/null +++ b/.github/workflows/biol1435-spring-tag.yml @@ -0,0 +1,56 @@ +name: tag-image-biol1435 +on: [workflow_dispatch] + +env: + CLASS: biol1435 + TARGET: r_julia + SQLITE: false + PYTHON_VERSION: "3.9" + PROJECT_ID: jupyterhub-docker-images + REGION: us-east1 + GAR_LOCATION: us-east1-docker.pkg.dev/jupyterhub-docker-images/all-classes/biol1435 + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3.5.3 + + - name: Set Up GCloud + uses: google-github-actions/setup-gcloud@v0.6.2 + with: + project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }} + service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }} + export_default_credentials: true + + - name: Create Julia Environment Files + if: env.TARGET == 'r_julia' + run: | + sudo --preserve-env=CLASS docker compose up julia_build + + - name: Upload Julia Env Files to Google Storage Bucket + if: env.TARGET == 'r_julia' + run: | + gsutil cp -r requirements/classes/biol1435/julia_env gs://jupyterhub-environment-files/spring-2025/biol1435/past/${GITHUB_SHA}/julia + gsutil cp -r requirements/classes/biol1435/julia_env gs://jupyterhub-environment-files/spring-2025/biol1435/latest/julia + + - name: Configure Docker + run: gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet + - name: Build JH Image + run: | + COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker compose up jh_image + docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:latest + docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/} + docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:${GITHUB_SHA} + docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:spring-2025 + - name: Push JH Image + run: | + docker push ${{ env.GAR_LOCATION }}:latest + docker push ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/} + docker push ${{ env.GAR_LOCATION }}:${GITHUB_SHA} + docker push ${{ env.GAR_LOCATION }}:spring-2025 + + - name: Upload Conda Env Files to Google Storage Bucket + run: | + gsutil cp -r requirements/out gs://jupyterhub-environment-files/spring-2025/biol1435/past/${GITHUB_SHA}/conda + gsutil cp -r requirements/out gs://jupyterhub-environment-files/spring-2025/biol1435/latest/conda \ No newline at end of file diff --git a/.github/workflows/biol1435.yml b/.github/workflows/biol1435.yml new file mode 100644 index 0000000..f38c51d --- /dev/null +++ b/.github/workflows/biol1435.yml @@ -0,0 +1,54 @@ +name: build-image-biol1435 +on: + push: + paths: + - 'requirements/classes/biol1435/**' + - 'Dockerfile' + - 'docker-compose.yml' + - 'scripts/**' + - '.github/workflows/biol1435.yml' + workflow_dispatch: + +env: + CLASS: biol1435 + TARGET: r_julia + SQLITE: false + PYTHON_VERSION: "3.9" + PROJECT_ID: jupyterhub-docker-images + REGION: us-east1 + GAR_LOCATION: us-east1-docker.pkg.dev/jupyterhub-docker-images/all-classes/biol1435 + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3.5.3 + + - name: Set Up GCloud + uses: google-github-actions/setup-gcloud@v0.6.2 + with: + project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }} + service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }} + export_default_credentials: true + + - name: Create Julia Environment Files + if: env.TARGET == 'r_julia' + run: | + sudo --preserve-env=CLASS docker compose up julia_build + + - name: Configure Docker + run: gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet + + - name: Build JH Image + run: | + COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker compose up jh_image + + - name: Tag JH Image + run: | + docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/} + docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:latest + + - name: Push JH Image + run: | + docker push ${{ env.GAR_LOCATION }}:latest + docker push ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/} \ No newline at end of file diff --git a/requirements/classes/biol1435/condarc b/requirements/classes/biol1435/condarc new file mode 100644 index 0000000..d2a8292 --- /dev/null +++ b/requirements/classes/biol1435/condarc @@ -0,0 +1,15 @@ +# channel locations. These override conda defaults, i.e., conda will +# search *only* the channels listed here, in the order given. +# Use "defaults" to automatically include all default channels. +# Non-url channels will be interpreted as Anaconda.org usernames +# (this can be changed by modifying the channel_alias key; see below). +# The default is just 'defaults'. +channels: + - conda-forge + +# Show channel URLs when displaying what is going to be downloaded +# and in 'conda list'. The default is False. +show_channel_urls: True + +# For more information about this file see: +# https://conda.io/docs/user-guide/configuration/use-condarc.html \ No newline at end of file diff --git a/requirements/classes/biol1435/packages.R b/requirements/classes/biol1435/packages.R new file mode 100644 index 0000000..e1dced3 --- /dev/null +++ b/requirements/classes/biol1435/packages.R @@ -0,0 +1,12 @@ +# Use this script to install packages via CRAN, for example: + +# NOTE: Code below shows how you install R packages from CRAN and Bioconductor. For CRAN packages, you can use +# the standard install.packages() function; for Bioconductor packages, however, you +# must first install BiocManager and then use that for installs. + +# install.packages("BiocManager", dependencies=TRUE, repos='http://cran.rstudio.com/') +# install.packages(c("ggplot2", "pheatmap", "RColorBrewer", "PoiClaClu", +# "patchwork", "tidyr", "GGally"), dependencies=TRUE, +# repos='http://cran.rstudio.com/') +# BiocManager::install(c("airway", "DESeq2", "vsn", "biomaRt", +# "AnnotationHub", "SummarizedExperiment")) diff --git a/requirements/classes/biol1435/requirements.jl b/requirements/classes/biol1435/requirements.jl new file mode 100644 index 0000000..87635a4 --- /dev/null +++ b/requirements/classes/biol1435/requirements.jl @@ -0,0 +1,5 @@ +const julia_packages = [ + "IJulia", # DO NOT REMOVE + # add class specific classes here: + + ] \ No newline at end of file diff --git a/requirements/classes/biol1435/requirements.pip.txt b/requirements/classes/biol1435/requirements.pip.txt new file mode 100644 index 0000000..27fbc34 --- /dev/null +++ b/requirements/classes/biol1435/requirements.pip.txt @@ -0,0 +1,2 @@ +# add class-specific classes here: +ete3 diff --git a/requirements/classes/biol1435/requirements.txt b/requirements/classes/biol1435/requirements.txt new file mode 100644 index 0000000..3a1f3e8 --- /dev/null +++ b/requirements/classes/biol1435/requirements.txt @@ -0,0 +1,77 @@ +# add class-specific packages here: +msprime +tskit +stdpopsim +pyslim +demes +demesdraw +sage + +# these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) +dask +pandas +numexpr +matplotlib +scipy +seaborn +scikit-learn +scikit-image +sympy +cython +patsy +statsmodels +cloudpickle +dill +numba +bokeh +sqlalchemy +hdf5 +vincent +beautifulsoup4 +protobuf +xlrd +bottleneck +pytables + +# these are the base r packages in the r-notebook image ( YOU PROBABLY WANT THESE IF YOUR TARGET IN DOCKER IS r_lang OR r_julia ) +# https://stat.ethz.ch/R-manual/R-devel/library/base/html/00Index.html +r-base=4.2.* +# https://github.com/topepo/caret/releases/tag/v6.0-93 +r-caret=6.* +# https://cran.r-project.org/web/packages/crayon/index.html +r-crayon=1.* +# https://cran.r-project.org/web/packages/devtools/index.html +r-devtools=2.* +# https://cran.r-project.org/web/packages/forecast/index.html +r-forecast=8.* +# https://cran.r-project.org/web/packages/hexbin/index.html +r-hexbin=1.* +# https://cran.r-project.org/web/packages/htmltools/index.html +r-htmltools=0.* +# https://cran.r-project.org/web/packages/htmlwidgets/index.html +r-htmlwidgets=1.* +# https://github.com/IRkernel/IRkernel/releases/tag/1.3.2 +r-irkernel=1.* +# https://cran.r-project.org/web/packages/nycflights13/index.html +r-nycflights13=1.* +# https://cran.r-project.org/web/packages/randomForest/index.html +r-randomforest=4.* +# https://cran.r-project.org/web/packages/RCurl/index.html +r-rcurl=1.98* +# https://cran.r-project.org/web/packages/rmarkdown/index.html +r-rmarkdown=2.* +# https://cran.r-project.org/web/packages/odbc/index.html +r-rodbc=1.* +# https://cran.r-project.org/web/packages/RSQLite/index.html +r-rsqlite=2.* +# https://cran.r-project.org/web/packages/shiny/index.html +r-shiny=1.* +# https://cran.r-project.org/web/packages/tidyverse/index.html +r-tidyverse +unixodbc=2.* +# https://cran.r-project.org/web/packages/tidymodels/index.html +r-tidymodels=1.* + +# required for environment and plugins ( DO NOT REMOVE THESE!!! ) +ipython +ipykernel