From 4154e6a880603072c77bc5395d5968a5270cf0de Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 5 Nov 2024 15:28:22 +0100
Subject: [PATCH] switch docker
---
workflows/deseq2/Dockerfile | 7 +++++++
workflows/deseq2/deseq2-localDocker-test.cwl | 16 ++++++++++++++++
workflows/deseq2/deseq2.cwl | 13 +++++++++----
workflows/deseq2/r-docker-test.cwl | 13 ++++++-------
4 files changed, 38 insertions(+), 11 deletions(-)
create mode 100644 workflows/deseq2/Dockerfile
create mode 100644 workflows/deseq2/deseq2-localDocker-test.cwl
diff --git a/workflows/deseq2/Dockerfile b/workflows/deseq2/Dockerfile
new file mode 100644
index 0000000..277379d
--- /dev/null
+++ b/workflows/deseq2/Dockerfile
@@ -0,0 +1,7 @@
+FROM quay.io/biocontainers/bioconductor-deseq2:1.42.0--r43hf17093f_2
+
+# Since our base image is an R docker base we will use BiocManager install
+
+RUN apt-get update && \
+ R -e "install.packages(c('BiocManager'), repos='https://cloud.r-project.org/');BiocManager::install('tximport')" && \
+ apt-get clean -y
\ No newline at end of file
diff --git a/workflows/deseq2/deseq2-localDocker-test.cwl b/workflows/deseq2/deseq2-localDocker-test.cwl
new file mode 100644
index 0000000..3e26cb8
--- /dev/null
+++ b/workflows/deseq2/deseq2-localDocker-test.cwl
@@ -0,0 +1,16 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerFile: {$include: "./Dockerfile"}
+ dockerImageId: "deseq-docker"
+requirements:
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [Rscript, --help]
+
+inputs: []
+
+outputs: []
diff --git a/workflows/deseq2/deseq2.cwl b/workflows/deseq2/deseq2.cwl
index 2f926aa..b35f8a4 100644
--- a/workflows/deseq2/deseq2.cwl
+++ b/workflows/deseq2/deseq2.cwl
@@ -1,8 +1,13 @@
+#!/usr/bin/env cwl-runner
+
cwlVersion: v1.2
class: CommandLineTool
-# hints:
-# DockerRequirement:
-# dockerPull: r-base:4.4.2
+hints:
+ # DockerRequirement:
+ # dockerPull: quay.io/biocontainers/bioconductor-deseq2:1.42.0--r43hf17093f_2
+ DockerRequirement:
+ dockerFile: {$include: "./Dockerfile"}
+ dockerImageId: "deseq-docker"
requirements:
- class: InitialWorkDirRequirement
listing:
@@ -11,7 +16,7 @@ requirements:
$include: deseq2.R
- class: NetworkAccess
networkAccess: true
-baseCommand: [RScript, deseq2.R]
+baseCommand: [Rscript, deseq2.R]
inputs:
inKallistoResults:
type: Directory
diff --git a/workflows/deseq2/r-docker-test.cwl b/workflows/deseq2/r-docker-test.cwl
index 3b26279..b964a83 100644
--- a/workflows/deseq2/r-docker-test.cwl
+++ b/workflows/deseq2/r-docker-test.cwl
@@ -1,15 +1,14 @@
+#!/usr/bin/env cwl-runner
+
cwlVersion: v1.2
class: CommandLineTool
requirements:
- - class: NetworkAccess
- networkAccess: true
- # - class: DockerRequirement
- # dockerPull: r-base:4.4.2
+ - class: DockerRequirement
+ dockerPull: quay.io/biocontainers/bioconductor-deseq2:1.42.0--r43hf17093f_2
-baseCommand: [RScript, --help]
+baseCommand: [Rscript, --help]
inputs: []
-
+
outputs: []
-
\ No newline at end of file
--
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