From 4c59c4a5b130b2c168e6bebf1534774c3d38ae83 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Wed, 26 Feb 2025 17:25:28 +0000
Subject: [PATCH] Pipeline now uses submodule for fork of recipe repo

---
 Jenkinsfile | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 97e754d..f1a169a 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -6,6 +6,12 @@ pipeline {
             inheritFrom 'miniforge'
         }
     }
+    environment {
+        TOOL_VER = """${sh(
+                returnStdout: true,
+                script: 'python pypi_latest_ver.py autoBIGS.engine'
+            )}"""
+    }
     stages {
         stage("prepare") {
             parallel {
@@ -16,7 +22,7 @@ pipeline {
                         sh 'git submodule init'
                         sh 'git submodule update'
                         dir('auto-updated-bioconda-recipes') {
-                            sh 'git checkout update-autobigs-engine'
+                            sh 'git checkout -b update-autobigs-engine-${TOOL_VER}'
                         }
                     }
                 }
@@ -54,7 +60,7 @@ pipeline {
                     }
                     steps {
                         dir('auto-updated-bioconda-recipes') {
-                            sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
+                            sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to ${TOOL_VER}."'
                             sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
                         }
                     }