diff --git a/workflows/sleuth/Dockerfile b/workflows/sleuth/Dockerfile deleted file mode 100644 index 39a6609301f9954da43bf426be379cfda98e5f85..0000000000000000000000000000000000000000 --- a/workflows/sleuth/Dockerfile +++ /dev/null @@ -1,29 +0,0 @@ -# Use an official R base image -FROM rocker/r-ver:4.1.3 - -# Install system dependencies for R packages and other utilities -RUN apt-get update && apt-get install -y \ - libcurl4-openssl-dev \ - libssl-dev \ - libxml2-dev \ - git \ - build-essential \ - && rm -rf /var/lib/apt/lists/* - -# Install BiocManager -RUN R -e "install.packages('BiocManager')" - -# Install Bioconductor version 3.14 -RUN R -e "BiocManager::install(version = '3.11')" - -# Install sleuth from Bioconductor -RUN R -e "BiocManager::install('sleuth')" - -# Install other necessary CRAN packages -RUN R -e "install.packages('jsonlite', repos='https://cran.r-project.org')" - -# Set the working directory to /app -WORKDIR /app - -# Default command to run when the container starts -CMD ["R"] diff --git a/workflows/sleuth/workflow.cwl b/workflows/sleuth/workflow.cwl index 8163e27b260d56b501b3e5f0ad8a95ffb4586649..4a8add08556780341d42af5b5488691ea8608107 100644 --- a/workflows/sleuth/workflow.cwl +++ b/workflows/sleuth/workflow.cwl @@ -4,9 +4,6 @@ cwlVersion: v1.2 class: CommandLineTool hints: - # DockerRequirement: - # dockerImageId: "sleuth" - # dockerFile: {$include: "Dockerfile"} DockerRequirement: dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0