Removed submodule

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "auto-updated-bioconda-recipes"]
-	path = auto-updated-bioconda-recipes
-	url = https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git

Jenkinsfile

@@ -6,6 +6,12 @@ pipeline {
             inheritFrom 'miniforge'
         }
     }
+    environment {
+        TOOL_VER = """${sh(
+                returnStdout: true,
+                script: 'python pypi_latest_ver.py autoBIGS.engine'
+            )}"""
+    }
     stages {
         stage("prepare") {
             parallel {
@@ -13,15 +19,15 @@ pipeline {
                     steps {
                         sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main'
                         sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes'
-                        sh 'git submodule init'
-                        sh 'git submodule update'
+                        sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
                         dir('auto-updated-bioconda-recipes') {
-                            sh 'git checkout update-autobigs-engine'
+                            sh 'git checkout -b update-autobigs-engine-${TOOL_VER}'
                         }
                     }
                 }
                 stage("conda") {
                     steps {
+                        sh 'conda config --add channels bioconda'
                         sh 'conda env update -n base --file environment.yml'
                     }
                 }
@@ -39,25 +45,21 @@ pipeline {
                 sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
             }
         }
-        stage("publish to bioconda") {
-            stages {
-                stage('lint') {
-                    steps {
-                        dir('auto-updated-bioconda-recipes') {
-                            sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
-                        }
-                    }
+        stage('lint') {
+            steps {
+                dir('auto-updated-bioconda-recipes') {
+                    sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
                 }
-                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'
-                        }
-                    }
+            }
+        }
+        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 ${TOOL_VER}."'
+                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine-${TOOL_VER}'
                 }
             }
         }