From e846c61d669d1db985c47ed66da8b724c4e52c96 Mon Sep 17 00:00:00 2001
From: Boas van der Putten <32385917+boasvdp@users.noreply.github.com>
Date: Fri, 9 Jun 2023 16:33:31 +0200
Subject: [PATCH] fix env name

---
 run_pipeline.sh | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/run_pipeline.sh b/run_pipeline.sh
index 215a646..84710eb 100755
--- a/run_pipeline.sh
+++ b/run_pipeline.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Wrapper for juno AMR pipeline
+# Wrapper for juno cgmlst pipeline
 
 set -euo pipefail
 
@@ -47,6 +47,13 @@ export -f __conda_activate
 export -f __conda_reactivate
 export -f __conda_hashr
 
+#----------------------------------------------#
+# Create the environment
+
+# we can use the base installation of mamba to create the environment. 
+# Swapping to a parent env is not necessary anymore.
+mamba env create -f envs/juno_cgmlst.yaml --name pipeline_env
+conda activate pipeline_env
 
 if [ ! -z ${irods_runsheet_sys__runsheet__lsf_queue} ]; then
     QUEUE="${irods_runsheet_sys__runsheet__lsf_queue}"