From 87c3766e807a07b79660b813191175def8e40dc6 Mon Sep 17 00:00:00 2001 From: Joselynn Wallace Date: Wed, 24 Apr 2024 09:46:02 -0400 Subject: [PATCH 1/2] updating the ccv_bootcamp workflow and requirements files for summer 2024 --- .github/workflows/ccv_bootcamp-summer-tag.yml | 22 ++-- .github/workflows/ccv_bootcamp.yml | 15 +-- requirements/classes/ccv_bootcamp/packages.R | 117 +++++------------- .../classes/ccv_bootcamp/requirements.jl | 4 +- .../classes/ccv_bootcamp/requirements.pip.txt | 2 +- .../classes/ccv_bootcamp/requirements.txt | 18 +-- 6 files changed, 62 insertions(+), 116 deletions(-) diff --git a/.github/workflows/ccv_bootcamp-summer-tag.yml b/.github/workflows/ccv_bootcamp-summer-tag.yml index 593c92a0..74c84e68 100644 --- a/.github/workflows/ccv_bootcamp-summer-tag.yml +++ b/.github/workflows/ccv_bootcamp-summer-tag.yml @@ -4,17 +4,17 @@ on: [workflow_dispatch] env: CLASS: ccv_bootcamp TARGET: r_julia - SQLITE: true - PYTHON_VERSION: 3.7 + SQLITE: false + PYTHON_VERSION: "3.9.17" jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - #https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/ + - uses: actions/checkout@v3.5.3 + - name: Set Up GCloud - uses: google-github-actions/setup-gcloud@v0.6.0 + uses: google-github-actions/setup-gcloud@v0.6.2 with: project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }} service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }} @@ -28,8 +28,8 @@ jobs: - name: Upload Julia Env Files to Google Storage Bucket if: env.TARGET == 'r_julia' run: | - gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/past/${GITHUB_SHA}/julia - gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/latest/julia + gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/past/${GITHUB_SHA}/julia + gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/latest/julia - name: Configure Docker run: gcloud auth configure-docker @@ -40,13 +40,13 @@ jobs: docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_REF##*/} docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_SHA} docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:latest - docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2023 + docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2024 docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:latest - docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2023 + docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2024 docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_REF##*/} docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_SHA} - name: Upload Conda Env Files to Google Storage Bucket run: | - gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/past/${GITHUB_SHA}/conda - gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/latest/conda + gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/past/${GITHUB_SHA}/conda + gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/latest/conda \ No newline at end of file diff --git a/.github/workflows/ccv_bootcamp.yml b/.github/workflows/ccv_bootcamp.yml index 2502c89c..1da73a13 100644 --- a/.github/workflows/ccv_bootcamp.yml +++ b/.github/workflows/ccv_bootcamp.yml @@ -12,16 +12,17 @@ on: env: CLASS: ccv_bootcamp TARGET: r_julia - SQLITE: true - PYTHON_VERSION: 3.7 + SQLITE: false + PYTHON_VERSION: "3.9.17" jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v3.5.3 + - name: Set Up GCloud - uses: google-github-actions/setup-gcloud@v0.6.0 + 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 }} @@ -34,9 +35,9 @@ jobs: - name: Configure Docker run: gcloud auth configure-docker -# - uses: satackey/action-docker-layer-caching@v0.0.11 -# # Ignore the failure of a step and avoid terminating the job. -# continue-on-error: true + - uses: satackey/action-docker-layer-caching@v0.0.11 + # Ignore the failure of a step and avoid terminating the job. + continue-on-error: true - name: Build and Push JH Image run: | COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image diff --git a/requirements/classes/ccv_bootcamp/packages.R b/requirements/classes/ccv_bootcamp/packages.R index a66389ca..5ac4bb76 100644 --- a/requirements/classes/ccv_bootcamp/packages.R +++ b/requirements/classes/ccv_bootcamp/packages.R @@ -1,90 +1,35 @@ +# 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")) + install.packages("BiocManager", dependencies=TRUE, repos='http://cran.rstudio.com/') install.packages(c("tidyverse"), dependencies=TRUE, repos='http://cran.rstudio.com/') -install.packages(c( -"ape", -"arrow", -"deldir", -"devtools", -"doMC", -"doRNG", -"DT", -"enrichR", -"ggrepel", -"hdf5r", -"kableExtra", -"knitr", -"maps", -"Matrix", -"metap", -"mixtools", -"NMF", -"openxlsx", -"parallel", -"patchwork", -"pdftools", -"pheatmap", -"plotly", -"PoiClaClu", -"purrr", -"R.utils", -"R2HTML", -"RColorBrewer", -"RcppArmadillo", -"remotes", -"Rfast2", -"rgeos", -"rsvd", -"Rtsne", -"sctransform", -"Seurat", -"spatstat.explore", -"spatstat.geom", -"stringr", -"VGAM", -"viridis", -"zoo"), - repos = "http://cran.rstudio.com/", - dependencies = TRUE) -BiocManager::install(c( -"airpart", -"airway", -"AnnotationHub", -"AUCell", -"batchelor", -"Biobase", -"BiocGenerics", -"biomaRt", -"BSgenome", -"BSgenome.Hsapiens.UCSC.hg19", -"clusterProfiler", -"ComplexHeatmap", -"DelayedArray", -"DelayedMatrixStats", -"DESeq2", -"DOSE", -"enrichplot", -"ensembldb", -"GENIE3", -"GenomicFeatures", -"GenomeInfoDb", -"GenomicRanges", -"glmGamPoi", -"IRanges", -"JASPAR2018", -"limma", -"MAST", -"monocle", -"multtest", -"RcisTarget", -"RnaSeqSampleSize", -"rtracklayer", -"S4Vectors", -"scater", -"SingleCellExperiment", -"SummarizedExperiment", -"TFBSTools", -"vsn", -"WGCNA")) +install.packages(c( "ape", "arrow", "deldir", "devtools", "doMC", + "doRNG", "DT", "enrichR", "ggrepel", "hdf5r", + "kableExtra", "knitr", "maps", "Matrix", "metap", + "mixtools", "NMF", "openxlsx", "parallel", "patchwork", + "pdftools", "pheatmap", "plotly", "PoiClaClu", "purrr", + "R.utils", "R2HTML", "RColorBrewer", "RcppArmadillo", "remotes", + "Rfast2", "rgeos", "rsvd", "Rtsne", "sctransform", "Seurat", + "spatstat.explore", "spatstat.geom", "stringr", "VGAM", "viridis", + "zoo"), repos = "http://cran.rstudio.com/", dependencies = TRUE) +BiocManager::install(c("airpart", "airway", "AnnotationHub", "AUCell", "batchelor", + "Biobase", "BiocGenerics", "biomaRt", "BSgenome", "BSgenome.Hsapiens.UCSC.hg19", + "clusterProfiler", "ComplexHeatmap", "DelayedArray", "DelayedMatrixStats", "DESeq2", + "DOSE", "enrichplot", "ensembldb", "GENIE3", "GenomicFeatures", + "GenomeInfoDb", "GenomicRanges", "glmGamPoi", "IRanges", + "JASPAR2022", "limma", "MAST", "monocle", "multtest", + "RcisTarget", "RnaSeqSampleSize", "rtracklayer", "S4Vectors", "scater", + "SingleCellExperiment", "SummarizedExperiment", "TFBSTools", "vsn", "WGCNA")) remotes::install_github("mojaveazure/seurat-disk") remotes::install_github("satijalab/seurat-data") -remotes::install_github("brendankelly/micropower") +remotes::install_github("brendankelly/micropower") \ No newline at end of file diff --git a/requirements/classes/ccv_bootcamp/requirements.jl b/requirements/classes/ccv_bootcamp/requirements.jl index ed8bd3aa..09245a4b 100644 --- a/requirements/classes/ccv_bootcamp/requirements.jl +++ b/requirements/classes/ccv_bootcamp/requirements.jl @@ -1,5 +1,5 @@ const julia_packages = [ - "IJulia", # DO NOT REMOVE + "IJulia", # DO NOT REMOVE # add class specific classes here: "CSV", "DataFrames", @@ -35,4 +35,4 @@ const julia_packages = [ "MLDatasets", "StatsPlots", "Tidier" - ] + ] \ No newline at end of file diff --git a/requirements/classes/ccv_bootcamp/requirements.pip.txt b/requirements/classes/ccv_bootcamp/requirements.pip.txt index 95b939e5..43719b70 100644 --- a/requirements/classes/ccv_bootcamp/requirements.pip.txt +++ b/requirements/classes/ccv_bootcamp/requirements.pip.txt @@ -1,2 +1,2 @@ -# add class-specific packages here: +# add class-specific classes here: diff --git a/requirements/classes/ccv_bootcamp/requirements.txt b/requirements/classes/ccv_bootcamp/requirements.txt index 44219816..e0689d67 100644 --- a/requirements/classes/ccv_bootcamp/requirements.txt +++ b/requirements/classes/ccv_bootcamp/requirements.txt @@ -32,20 +32,20 @@ r-caret=6.* r-crayon=1.* r-devtools=2.* r-forecast=8.* -r-hexbin=1.28* -r-htmltools -r-htmlwidgets=1.5* +r-hexbin=1.* +r-htmltools=0.* +r-htmlwidgets=1.* r-irkernel=1.* -r-nycflights13=1.0* +r-nycflights13=1.* r-randomforest=4.* r-rcurl=1.98* r-rmarkdown=2.* -r-rodbc=1.3* -r-rsqlite=2.2* +r-rodbc=1.* +r-rsqlite=2.* r-shiny=1.* -r-tidyverse=1.3* -unixodbc=2.3.* -r-tidymodels +r-tidyverse +unixodbc=2.* +r-tidymodels=1.* # required for environment and plugins ( DO NOT REMOVE THESE!!! ) ipython From bcda1cc73997edbd3a80562bba75ada08cada5b5 Mon Sep 17 00:00:00 2001 From: Joselynn Wallace Date: Wed, 8 May 2024 09:40:21 -0400 Subject: [PATCH 2/2] update checkout to v4 --- .github/workflows/ccv_bootcamp-summer-tag.yml | 4 ++-- .github/workflows/ccv_bootcamp.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ccv_bootcamp-summer-tag.yml b/.github/workflows/ccv_bootcamp-summer-tag.yml index 74c84e68..f2ca2e61 100644 --- a/.github/workflows/ccv_bootcamp-summer-tag.yml +++ b/.github/workflows/ccv_bootcamp-summer-tag.yml @@ -11,7 +11,7 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3.5.3 + - uses: actions/checkout@v4 - name: Set Up GCloud uses: google-github-actions/setup-gcloud@v0.6.2 @@ -49,4 +49,4 @@ jobs: - name: Upload Conda Env Files to Google Storage Bucket run: | gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/past/${GITHUB_SHA}/conda - gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/latest/conda \ No newline at end of file + gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/latest/conda diff --git a/.github/workflows/ccv_bootcamp.yml b/.github/workflows/ccv_bootcamp.yml index 1da73a13..1716b4be 100644 --- a/.github/workflows/ccv_bootcamp.yml +++ b/.github/workflows/ccv_bootcamp.yml @@ -19,7 +19,7 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3.5.3 + - uses: actions/checkout@v4 - name: Set Up GCloud uses: google-github-actions/setup-gcloud@v0.6.2