From bd465bfd4304930dc5734b5df5cc2bd84f28db47 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 18 Mar 2025 17:19:43 +0100
Subject: [PATCH] rm dockerfile sleuth
---
workflows/sleuth/Dockerfile | 29 -----------------------------
workflows/sleuth/workflow.cwl | 3 ---
2 files changed, 32 deletions(-)
delete mode 100644 workflows/sleuth/Dockerfile
diff --git a/workflows/sleuth/Dockerfile b/workflows/sleuth/Dockerfile
deleted file mode 100644
index 39a6609..0000000
--- 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 8163e27..4a8add0 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
--
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