Merge branch 'main' of https://github.com/CCBR/spacesavers2

.gitattributes

@@ -0,0 +1 @@
+docs/*.html linguist-generated

.github/workflows/docker.yml

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+name: docker
+
+on:
+  push:
+    paths:
+      - .github/workflows/docker.yml
+      - "docker/**"
+  workflow_dispatch:
+
+jobs:
+  generate-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix-metadata: ${{ steps.metadata.outputs.matrix }}
+    steps:
+      - uses: hellofresh/action-changed-files@v3
+        id: metadata
+        with:
+          pattern: docker/(?P<image_dir>\w+)/.*
+          default-patterns: |
+            meta.yml
+            Dockerfile
+
+  update-docker:
+    needs: [generate-matrix]
+    strategy:
+      matrix: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata) }}
+    if: ${{ fromJson(needs.generate-matrix.outputs.matrix-metadata).include[0] }} # skip if the matrix is empty!
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pietrobolcato/action-read-yaml@1.0.0
+        id: metadata
+        with:
+          config: ${{ github.workspace }}/docker/${{ matrix.image_dir }}/meta.yml
+      - name: Get date
+        id: date
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> $GITHUB_OUTPUT
+      - name: Login to DockerHub
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        # only try building & pushing the container if parsing the metadata worked
+        if: ${{ steps.metadata.outputs['container'] != '' }}
+        with:
+          context: docker/${{ matrix.image_dir }}
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.metadata.outputs['container'] }}
+          build-args: |
+            BUILD_DATE=${{ steps.date.outputs.DATE }}
+            BUILD_TAG=${{ steps.metadata.outputs['version'] }}
+            REPONAME=${{ steps.metadata.outputs['image_name'] }}

.gitignore

@@ -1,9 +1,19 @@
-**/.koparde*
+**/.kopard*
 **/.DS_Store
 **/__pycache__
 **/.**.swp
 **/slurm-*
+
 # mkdocs documentation
 /site
 **/test.py
 **/test/
+
+# data
+/data/
+
+# R
+.Rproj.user
+*.Rproj
+.Rhistory
+/.quarto/

.pre-commit-config.yaml

@@ -1,16 +1,24 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html
+   )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
       - id: check-added-large-files
-      #- id: check-yaml
+        args: ['--maxkb=50000']
       - id: end-of-file-fixer
       - id: trailing-whitespace
   # spell check
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4
     hooks:
       - id: codespell
+        # https://github.com/codespell-project/codespell/issues/1498
   # Python formatting
   - repo: https://github.com/psf/black
     rev: 23.7.0
@@ -31,3 +39,5 @@ repos:
     rev: v2.3.0
     hooks:
       - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []

.prettierignore

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+**/.koparde*
+**/.DS_Store
+**/__pycache__
+**/.**.swp
+**/slurm-*
+
+# mkdocs documentation
+/site
+**/test.py
+**/test/
+
+# data
+/data/
+
+# R
+.Rproj.user
+*.Rproj

bin/render.R

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+#!/usr/bin/env Rscript
+rmarkdown::render("report.Rmd",
+  output_file = "docs/report.html",
+  params = list(input_dir = "data")
+)

bin/render_report_biowulf.sh

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+#!/usr/bin/env bash
+# to be executed from /data/CCBR_Pipeliner/Tools/spacesavers2/report
+# Usage: bash bin/render_report_biowulf.sh
+module load singularity
+SINGULARITY_CACHEDIR=/data/CCBR_Pipeliner/SIFS
+echo "cd /mnt && Rscript bin/render.R" |\
+    singularity exec -C -B $PWD:/mnt,/data/CCBR_Pipeliner/userdata/spacesavers2/:/mnt/data docker://nciccbr/spacesavers2:0.1.1 bash
+today=$(date +'%Y-%m-%d')
+cp docs/report.html docs/report_${today}.html

docker/spacesavers2/Dockerfile

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+FROM ubuntu:20.04
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+RUN mkdir -p /opt2 && mkdir -p /data2
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+RUN apt update && apt-get -y upgrade
+# Set the locale
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+		locales build-essential cmake cpanminus && \
+	localedef -i en_US -f UTF-8 en_US.UTF-8 && \
+	cpanm FindBin Term::ReadLine
+
+# install basic dependencies with apt-get
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+    build-essential \
+	figlet \
+	g++ \
+	gcc \
+	gfortran \
+	git \
+	libatlas-base-dev \
+	libblas-dev \
+	libboost-dev \
+	libbz2-dev \
+	libcurl4-openssl-dev \
+	libexpat1-dev \
+	libfreetype6-dev \
+	libgd-dev \
+	libgd-perl \
+	libglib2.0-dev \
+    libgpgme11-dev \
+	libgs-dev \
+	libgsl-dev \
+	libgsl0-dev \
+	libhtml-template-compiled-perl \
+	libicu-dev \
+	libjudy-dev \
+	liblapack-dev \
+	liblzma-dev \
+	libmysqlclient-dev \
+	libncurses-dev \
+	libopenmpi-dev \
+	libpng-dev \
+	librtmp-dev \
+    libseccomp-dev \
+	libssl-dev \
+	libtool \
+	libxml-libxml-debugging-perl \
+	libxml-opml-simplegen-perl \
+	libxml2-dev \
+	libxslt-dev \
+	make \
+	manpages-dev \
+	openjdk-17-jre-headless \
+	parallel \
+	pigz \
+    pkg-config \
+	python3-pip \
+    python3-dev \
+	rsync \
+    squashfs-tools \
+	unzip \
+    uuid-dev \
+	wget \
+	zlib1g \
+	zlib1g-dev \
+	zlibc
+
+# Install conda and give write permissions to conda folder
+RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
+    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
+ENV PATH="/opt2/conda/bin:$PATH"
+
+# install pandoc & R packages
+COPY environment.txt /data2/
+RUN mamba install -c conda-forge --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# install quarto
+ENV QUARTO_VERSION="1.3.450"
+ADD https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.tar.gz /opt2
+WORKDIR /opt2
+RUN tar -xzvf quarto-${QUARTO_VERSION}-linux-amd64.tar.gz
+ENV PATH="/opt2/quarto-${QUARTO_VERSION}/bin/:${PATH}"
+RUN quarto check
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

docker/spacesavers2/environment.txt

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+pandoc
+r-base=4.3.1
+r-DT
+r-RColorBrewer
+r-bslib=0.5.1
+r-crosstalk
+r-downlit
+r-dplyr
+r-fontawesome
+r-ggplot2
+r-glue
+r-here
+r-janitor
+r-knitr
+r-lubridate
+r-plotly
+r-purrr
+r-readr
+r-rlang
+r-rmarkdown
+r-scales
+r-shiny
+r-stringr
+r-tibble
+r-tidyr
+r-xml2

docker/spacesavers2/meta.yml

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+dockerhub_namespace: nciccbr
+image_name: spacesavers2
+version: 0.1.1
+container: "$(dockerhub_namespace)/$(image_name):$(version)"