From ae537382194345d026a80cb76b6b1983358dfe3d Mon Sep 17 00:00:00 2001
From: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
Date: Tue, 27 Jun 2023 12:49:02 +0200
Subject: [PATCH 1/2] Add Apptainer (Singularity) to Gitpod nf-core base image.

---
 nf_core/gitpod/gitpod.Dockerfile | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index 5fce2f055b..05ec55ea4b 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -3,6 +3,7 @@ FROM gitpod/workspace-base
 USER root
 
 # Install util tools.
+# software-properties-common is needed to add ppa support for Apptainer installation
 RUN apt-get update --quiet && \
     apt-get install --quiet --yes \
     apt-transport-https \
@@ -13,7 +14,13 @@ RUN apt-get update --quiet && \
     wget \
     curl \
     tree \
-    graphviz
+    graphviz \
+    software-properties-common
+
+# Install Apptainer (Singularity)
+RUN add-apt-repository -y ppa:apptainer/ppa && \
+    apt-get update --quiet && \
+    apt install -y apptainer
 
 # Install Conda
 RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
@@ -38,13 +45,13 @@ RUN conda config --add channels defaults && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base mamba && \
     mamba install --quiet --yes --name base \
-        nextflow \
-        nf-core \
-        nf-test \
-        black \
-        prettier \
-        pre-commit \
-        pytest-workflow && \
+    nextflow \
+    nf-core \
+    nf-test \
+    black \
+    prettier \
+    pre-commit \
+    pytest-workflow && \
     mamba clean --all -f -y
 
 # Update Nextflow

From ac6777a9888f9d275ac509e6c7c9efc9f7b3841d Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 29 Jun 2023 10:13:41 +0200
Subject: [PATCH 2/2] =?UTF-8?q?Phil=20likes=20indentation=20=F0=9F=A4=93?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 nf_core/gitpod/gitpod.Dockerfile | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index 05ec55ea4b..47b27bb514 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -45,13 +45,13 @@ RUN conda config --add channels defaults && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base mamba && \
     mamba install --quiet --yes --name base \
-    nextflow \
-    nf-core \
-    nf-test \
-    black \
-    prettier \
-    pre-commit \
-    pytest-workflow && \
+        nextflow \
+        nf-core \
+        nf-test \
+        black \
+        prettier \
+        pre-commit \
+        pytest-workflow && \
     mamba clean --all -f -y
 
 # Update Nextflow