From 619bf65026a7cee41575dd4858df831ada1cde4e Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Wed, 20 Nov 2024 01:46:47 -0800
Subject: [PATCH] vEcoli instead of vivarium-ecoli

---
 runscripts/container/build-runtime.sh   | 2 +-
 runscripts/container/build-wcm.sh       | 4 ++--
 runscripts/container/runtime/Dockerfile | 2 +-
 runscripts/nextflow/colony.nf           | 2 +-
 runscripts/nextflow/config.template     | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/runscripts/container/build-runtime.sh b/runscripts/container/build-runtime.sh
index 608055c8b..2d9af708d 100755
--- a/runscripts/container/build-runtime.sh
+++ b/runscripts/container/build-runtime.sh
@@ -3,7 +3,7 @@
 # image with requirements.txt installed. If using Cloud Build, store the
 # built image in the "vecoli" folder in the Google Artifact Registry.
 #
-# ASSUMES: The current working dir is the vivarium-ecoli/ project root.
+# ASSUMES: The current working dir is the vEcoli/ project root.
 
 set -eu
 
diff --git a/runscripts/container/build-wcm.sh b/runscripts/container/build-wcm.sh
index 48da9133a..692b58fbb 100755
--- a/runscripts/container/build-wcm.sh
+++ b/runscripts/container/build-wcm.sh
@@ -1,9 +1,9 @@
 #!/bin/sh
 # Use Google Cloud Build or local Docker install to build a personalized image
-# with current state of the vivarium-ecoli repo. If using Cloud Build, store
+# with current state of the vEcoli repo. If using Cloud Build, store
 # the built image in the "vecoli" folder in the Google Artifact Registry.
 #
-# ASSUMES: The current working dir is the vivarium-ecoli/ project root.
+# ASSUMES: The current working dir is the vEcoli/ project root.
 
 set -eu
 
diff --git a/runscripts/container/runtime/Dockerfile b/runscripts/container/runtime/Dockerfile
index 1d2b8779b..cd81997e4 100644
--- a/runscripts/container/runtime/Dockerfile
+++ b/runscripts/container/runtime/Dockerfile
@@ -1,7 +1,7 @@
 # Container image #1: wcm-runtime.
 # This Dockerfile builds the runtime environment for the whole cell model.
 #
-# To build this image locally from the vivarium-ecoli/ project root directory:
+# To build this image locally from the vEcoli/ project root directory:
 #
 #     > docker build -f cloud/docker/runtime/Dockerfile -t ${USER}-wcm-runtime .
 #
diff --git a/runscripts/nextflow/colony.nf b/runscripts/nextflow/colony.nf
index 41ca6fd14..7caa6d63d 100644
--- a/runscripts/nextflow/colony.nf
+++ b/runscripts/nextflow/colony.nf
@@ -9,7 +9,7 @@ process colony {
 
     script:
     """
-    python /vivarium-ecoli/ecoli/experiments/ecoli_engine_process.py --config $config --sim_data_path $sim_data --initial_state_file $initial_state
+    python /vEcoli/ecoli/experiments/ecoli_engine_process.py --config $config --sim_data_path $sim_data --initial_state_file $initial_state
     STATUS=$?
     """
 
diff --git a/runscripts/nextflow/config.template b/runscripts/nextflow/config.template
index db9ea685f..43b86e026 100644
--- a/runscripts/nextflow/config.template
+++ b/runscripts/nextflow/config.template
@@ -25,7 +25,7 @@ profiles {
         google.location = 'us-west1'
         google.batch.spot = true
         docker.enabled = true
-        params.projectRoot = '/vivarium-ecoli'
+        params.projectRoot = '/vEcoli'
         params.publishDir = "PUBLISH_DIR"
         process.maxRetries = 1
         // Check Google Cloud latest spot pricing / performance