From cd033e99e5291d01b1f18322c2cc3124f55a34a8 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Mon, 24 Feb 2025 17:52:21 +0000
Subject: [PATCH] Changed devcontainer

---
 .devcontainer/Dockerfile        | 16 ++++++++++++++++
 .devcontainer/devcontainer.json | 12 +++++++-----
 .devcontainer/noop.txt          |  3 +++
 Jenkinsfile                     |  3 +--
 environment.yml                 |  7 +++++++
 5 files changed, 34 insertions(+), 7 deletions(-)
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/noop.txt
 create mode 100644 environment.yml

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 0000000..808f11b
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,16 @@
+FROM mcr.microsoft.com/devcontainers/miniconda:1-3
+
+# Copy environment.yml (if found) to a temp location so we update the environment. Also
+# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
+COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
+RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
+    && rm -rf /tmp/conda-tmp
+
+# [Optional] Uncomment to install a different version of Python than the default
+# RUN conda install -y python=3.6 \
+#     && pip install --no-cache-dir pipx \
+#     && pipx reinstall-all
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ce3acb4..43d26c5 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,9 +1,11 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/python
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
 {
-	"name": "Python 3",
-	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+	"name": "Miniconda (Python 3)",
+	"build": { 
+		"context": "..",
+		"dockerfile": "Dockerfile"
+	}
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -12,7 +14,7 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt"
+	// "postCreateCommand": "python --version",
 
 	// Configure tool-specific properties.
 	// "customizations": {},
diff --git a/.devcontainer/noop.txt b/.devcontainer/noop.txt
new file mode 100644
index 0000000..abee195
--- /dev/null
+++ b/.devcontainer/noop.txt
@@ -0,0 +1,3 @@
+This file is copied into the container along with environment.yml* from the
+parent folder. This is done to prevent the Dockerfile COPY instruction from 
+failing if no environment.yml is found.
\ No newline at end of file
diff --git a/Jenkinsfile b/Jenkinsfile
index adf8824..9f3b18a 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -10,11 +10,10 @@ pipeline {
     stages {
         stage ("install") {
             steps {
-                sh 'conda install python==3.12.7 pip -y -q'
+                sh 'conda env update -n base --file environment.yml'
                 sh 'useradd galaxy -m'
                 sh 'apt-get update'
                 sh 'apt-get install sudo -y'
-                sh 'pip install -r requirements.txt'
             }
         }
         stage ("lint") {
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..7d21ca9
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,7 @@
+name: base
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - python==3.12
+  - planemo
\ No newline at end of file