Removed submodule

Jenkinsfile

@@ -6,21 +6,28 @@ pipeline {
             inheritFrom 'miniforge'
         }
     }
+    environment {
+        TOOL_VER = """${sh(
+                returnStdout: true,
+                script: 'python pypi_latest_ver.py autoBIGS.engine'
+            )}"""
+    }
     stages {
         stage("prepare") {
             parallel {
                 stage("recipes repo") {
                     steps {
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main'
+                        sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes'
                         sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
                         dir('auto-updated-bioconda-recipes') {
-                            sh 'git pull'
-                            sh 'git pull origin update-autobigs-engine'
-                            sh 'git checkout update-autobigs-engine'
+                            sh 'git checkout -b update-autobigs-engine-${TOOL_VER}'
                         }
                     }
                 }
                 stage("conda") {
                     steps {
+                        sh 'conda config --add channels bioconda'
                         sh 'conda env update -n base --file environment.yml'
                     }
                 }
@@ -33,26 +40,26 @@ pipeline {
                 sh 'cp -r autobigs-engine/* auto-updated-bioconda-recipes/recipes/autobigs-engine/.'
             }
         }
-        stage("lint") {
+        stage("build") {
+            steps {
+                sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
+            }
+        }
+        stage('lint') {
             steps {
                 dir('auto-updated-bioconda-recipes') {
                     sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
                 }
             }
         }
-        stage("build") {
-            steps {
-                sh 'conda build bioconda-utils/recipes/autobigs-engine'
-            }
-        }
-        stage("commit") {
+        stage('commit') {
             environment {
                 TOKEN = credentials('github.com')
             }
             steps {
                 dir('auto-updated-bioconda-recipes') {
-                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
-                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-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-${TOOL_VER}'
                 }
             }
         }

environment.yml

@@ -8,3 +8,5 @@ dependencies:
   - git
   - bioconda-utils
   - python=3.10.*
+  - curl
+  - conda-verify