From ca8ecc0478fbf88b9cf3010ee248432142525a7f Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Wed, 19 Feb 2025 16:55:58 +0000
Subject: [PATCH] Added way to fetch bioconda dependency

---
 .gitignore      |  2 +-
 Jenkinsfile     | 16 +++++++++++-----
 environment.yml |  3 ---
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index 0063e68..a1abd8d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -176,4 +176,4 @@ pyrightconfig.json
 # End of https://www.toptal.com/developers/gitignore/api/python
 
 autobigs-engine/*
-bioconda-recipes/*
\ No newline at end of file
+auto-updated-bioconda-recipes/*
\ No newline at end of file
diff --git a/Jenkinsfile b/Jenkinsfile
index 1d5b3d6..313f7ed 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -24,26 +24,32 @@ pipeline {
                         sh 'conda env update -n base --file environment.yml'
                     }
                 }
+                stage("generate recipe") {
+                    sh 'grayskull pypi autoBIGS.cli --maintainers "Harrison Deng"'
+                    sh 'python patch_recipe.py'
+                }
             }
         }
-        stage("generate recipe") {
+        stage("update repo") {
             steps {
-                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'
+                container(miniforge3) {
+                    dir('auto-updated-bioconda-recipes') {
+                        sh 'conda -n install python=3.10 bioconda-utils'
+                        sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
+                    }
                 }
             }
         }
         stage("build") {
             steps {
                 dir('auto-updated-bioconda-recipes') {
+                    sh 'conda install autobigs-engine=$(python ../pypi_latest_ver.py autoBIGS.engine)'
                     sh 'conda build recipes/autobigs-cli'
                 }
             }
diff --git a/environment.yml b/environment.yml
index 7ea8054..5cbd326 100644
--- a/environment.yml
+++ b/environment.yml
@@ -6,6 +6,3 @@ dependencies:
   - conda-build
   - grayskull
   - git
-  - bioconda-utils
-  - python=3.10.*
-  - autobigs-engine
\ No newline at end of file