updated dependency version, and Docker instructions vignette

csbg · Sep 28, 2024 · bf071d8 · bf071d8
1 parent d85a2df
commit bf071d8
Show file tree

Hide file tree

Showing 28 changed files with 1,006 additions and 283 deletions.
diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -2,7 +2,11 @@
 FROM rocker/rstudio:4.4.0
 
 # Create directories for the R package, data, output, and workspace
-RUN mkdir -p /home/rstudio/input /home/rstudio/output /app /log /renv/library
+RUN mkdir -p /home/rstudio/input /home/rstudio/output /app /log 
+
+# Ensure the rstudio user has ownership of input and output directories
+RUN chown -R rstudio:rstudio /home/rstudio/input /home/rstudio/output && \
+    chmod -R 755 /home/rstudio/input /home/rstudio/output
 
 # Install system dependencies
 RUN apt-get update && apt-get install -y \
@@ -25,19 +29,19 @@ RUN apt-get update && apt-get install -y \
 # Set the working directory 
 WORKDIR /app
 
-# Ensure BiocManager and remotes packages are installed
+# Ensure BiocManager and remotes packages are installed in the custom library
 RUN R -e "install.packages('BiocManager'); install.packages('remotes')" 2>&1 | tee /log/biocmanager_remotes_install_log.txt
 
-# Install the SplineOmics package from GitHub
+# Install the SplineOmics package from GitHub in the custom library
 RUN R -e "remotes::install_github('csbg/SplineOmics', ref = '0.1.0', dependencies = TRUE, force = TRUE)" 2>&1 | tee /log/splineomics_install_log.txt
 
-# Install Bioconductor dependencies via BiocManager
+# Install Bioconductor dependencies via BiocManager in the custom library
 RUN R -e "BiocManager::install(c('ComplexHeatmap', 'limma', 'edgeR', 'clusterProfiler'), force = TRUE)" 2>&1 | tee /log/bioconductor_install_log.txt
 
-# Install necessary R packages (conflicted, here, readxl, readr)
+# Install necessary R packages in the custom library
 RUN R -e "install.packages(c('conflicted', 'here', 'readxl', 'readr'))" 2>&1 | tee /log/required_packages_install_log.txt
 
-# Write installed R packages and versions to a file
+# Write installed R packages and versions to a file in the default library
 RUN R -e "installed_packages <- installed.packages(); write.csv(installed_packages, '/log/installed_r_packages.csv', row.names = FALSE)"
 
 # Write installed operating system packages to a file
@@ -47,5 +51,5 @@ RUN dpkg-query -Wf '${Package} ${Version}\n' > /log/installed_os_packages.txt
 CMD ["/init"]
 
 # To build the image, run the following command in the dir where this Dockerfile is located:
-# docker build -t thomasrauter/splineomics:0.1.0 .
+# docker build --no-cache -t thomasrauter/splineomics:0.1.0 .
 
diff --git a/docker/input/hallo.txt b/docker/input/hallo.txt
diff --git a/docs/articles/Docker-instructions.html b/docs/articles/Docker-instructions.html
diff --git a/docs/articles/get-started.html b/docs/articles/get-started.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
   Docker_permission_denied: Docker_permission_denied.html
   Docker-instructions: Docker-instructions.html
   get-started: get-started.html
-last_built: 2024-09-23T14:59Z
+last_built: 2024-09-28T15:20Z
 urls:
   reference: https://csbg.github.io/SplineOmics/reference
   article: https://csbg.github.io/SplineOmics/articles
diff --git a/docs/reference/InputControl.html b/docs/reference/InputControl.html
diff --git a/docs/reference/bind_data_with_annotation.html b/docs/reference/bind_data_with_annotation.html
diff --git a/docs/reference/build_cluster_hits_report.html b/docs/reference/build_cluster_hits_report.html
diff --git a/docs/reference/cluster_hits.html b/docs/reference/cluster_hits.html
diff --git a/docs/reference/create_p_value_histogram.html b/docs/reference/create_p_value_histogram.html
diff --git a/docs/reference/create_splineomics.html b/docs/reference/create_splineomics.html
diff --git a/docs/reference/generate_report_html.html b/docs/reference/generate_report_html.html