From c0a5c343806467593cf4da14a406580112cf5160 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Wed, 26 Feb 2025 17:22:14 +0000
Subject: [PATCH] Updated pipeline to use submodule of recipe repo fork

---
 .gitmodules                   |  3 ++
 Jenkinsfile                   | 52 +++++++++++++++++++++--------------
 auto-updated-bioconda-recipes |  1 +
 3 files changed, 35 insertions(+), 21 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 auto-updated-bioconda-recipes

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..4141163
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "auto-updated-bioconda-recipes"]
+	path = auto-updated-bioconda-recipes
+	url = https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git
diff --git a/Jenkinsfile b/Jenkinsfile
index 653e94a..baa2741 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -6,14 +6,23 @@ pipeline {
             inheritFrom 'miniforge'
         }
     }
+    environment {
+        TOOL_VER = """${sh(
+                returnStdout: true,
+                script: 'python pypi_latest_ver.py autoBIGS.cli'
+            )}"""
+    }
     stages {
         stage("prepare") {
             parallel {
                 stage("recipes repo") {
                     steps {
-                        sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.cli-bioconda_main'
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.cli-bioconda_main/auto-updated-bioconda-recipes'
+                        sh 'git submodule init'
+                        sh 'git submodule update'
                         dir('auto-updated-bioconda-recipes') {
-                            sh 'git checkout update-autobigs-cli'
+                            sh 'git checkout -b update-autobigs-cli-${TOOL_VER}'
                         }
                     }
                 }
@@ -30,31 +39,32 @@ pipeline {
                 sh 'grayskull pypi autoBIGS.cli --maintainers "Harrison Deng"'
                 sh 'python patch_recipe.py'
                 sh 'cp -r autobigs-cli/* auto-updated-bioconda-recipes/recipes/autobigs-cli/.'
-                sh 'cat auto-updated-bioconda-recipes/recipes/autobigs-cli/meta.yaml'
-            }
-        }
-        stage("lint") {
-            steps {
-                dir('auto-updated-bioconda-recipes') {
-                    sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
-                }
             }
         }
         stage("build") {
             steps {
-                dir('auto-updated-bioconda-recipes') {
-                    sh 'conda build recipes/autobigs-cli'
-                }
+                sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-cli --output-folder ./conda-bld'
             }
         }
-        stage("commit") {
-            environment {
-                TOKEN = credentials('github.com')
-            }
-            steps {
-                dir('auto-updated-bioconda-recipes') {
-                    sh 'git commit -a -m "Automatically updated autobigs-cli bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.cli)."'
-                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-cli'
+        stage("publish to bioconda") {
+            stages {
+                stage('lint') {
+                    steps {
+                        dir('auto-updated-bioconda-recipes') {
+                            sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
+                        }
+                    }
+                }
+                stage('commit') {
+                    environment {
+                        TOKEN = credentials('github.com')
+                    }
+                    steps {
+                        dir('auto-updated-bioconda-recipes') {
+                            sh 'git commit -a -m "Automatically updated autobigs-cli bioconda recipe to ${TOOL_VER}."'
+                            sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-cli'
+                        }
+                    }
                 }
             }
         }
diff --git a/auto-updated-bioconda-recipes b/auto-updated-bioconda-recipes
new file mode 160000
index 0000000..d3a7205
--- /dev/null
+++ b/auto-updated-bioconda-recipes
@@ -0,0 +1 @@
+Subproject commit d3a720566fbbc63e32571ade8d643a6f6b1a4e25