From 1d61c6c6067e3dc39e94ba759fb4303353f955ce Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 22 Jan 2026 10:48:55 -0500
Subject: [PATCH 1/4] Don't exit if successful

---
 worker/run-worker.sh | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/worker/run-worker.sh b/worker/run-worker.sh
index fb0deee..84dd0ee 100644
--- a/worker/run-worker.sh
+++ b/worker/run-worker.sh
@@ -59,8 +59,7 @@ if [[ ${USE_PLUGINS} == 'True' ]]; then
   if [[ ${PLUGINS_COMMIT} != 'False' ]]; then
     echo "Checking out specific CellProfiler-plugins commit."
     cd CellProfiler-plugins
-    git checkout ${PLUGINS_COMMIT} || echo "No such commit, branch, or version; failing here." & exit 1
-    cd ..
+    git checkout ${PLUGINS_COMMIT} & cd .. & echo "checkout successful" || (echo "No such commit, branch, or version; failing here." & exit 1)
   fi 
   if [[ ${INSTALL_REQUIREMENTS} == 'True' ]]; then
     cd CellProfiler-plugins
@@ -69,11 +68,11 @@ if [[ ${USE_PLUGINS} == 'True' ]]; then
     fi
     if [[ -d "active_plugins" ]]; then
       echo "Installing CellProfiler-plugins requirements."
-      pip install -e . ${REQUIREMENTS} || echo "Requirements install failed." & exit 1
+      pip install -e . ${REQUIREMENTS} || (echo "Requirements install failed." & exit 1)
       cd ..
     else 
       echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements."
-      pip install -r ${REQUIREMENTS} || echo "Requirements file not present or install failed; failing here." & exit 1
+      pip install -r ${REQUIREMENTS} || (echo "Requirements file not present or install failed; failing here." & exit 1)
       cd ..
     fi
   fi

From fb7b3336f4b4c04c56856202e4e376804f66fbc7 Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 22 Jan 2026 13:24:42 -0500
Subject: [PATCH 2/4] add sleep, reorg a bit

---
 worker/run-worker.sh | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/worker/run-worker.sh b/worker/run-worker.sh
index 84dd0ee..1226117 100644
--- a/worker/run-worker.sh
+++ b/worker/run-worker.sh
@@ -47,19 +47,13 @@ python3.8 instance-monitor.py &
 # 5. UPDATE AND/OR INSTALL PLUGINS
 if [[ ${USE_PLUGINS} == 'True' ]]; then
   if [[ ${UPDATE_PLUGINS} == 'True' ]]; then
-    echo "Updating CellProfiler-plugins."
-    cd CellProfiler-plugins
-    git fetch --all
-    git pull
-    cd ..
+    (echo "Updating CellProfiler-plugins." & cd CellProfiler-plugins & git fetch --all & git pull & cd ..)
   fi
   if [[ -z "$PLUGINS_COMMIT" ]]; then
     PLUGINS_COMMIT='False'
   fi
   if [[ ${PLUGINS_COMMIT} != 'False' ]]; then
-    echo "Checking out specific CellProfiler-plugins commit."
-    cd CellProfiler-plugins
-    git checkout ${PLUGINS_COMMIT} & cd .. & echo "checkout successful" || (echo "No such commit, branch, or version; failing here." & exit 1)
+    (echo "Checking out specific CellProfiler-plugins commit." & cd CellProfiler-plugins & git checkout ${PLUGINS_COMMIT} & cd .. & echo "checkout successful" & sleep 3) || (echo "No such commit, branch, or version; failing here." & exit 1)
   fi 
   if [[ ${INSTALL_REQUIREMENTS} == 'True' ]]; then
     cd CellProfiler-plugins
@@ -67,13 +61,9 @@ if [[ ${USE_PLUGINS} == 'True' ]]; then
       REQUIREMENTS = $REQUIREMENTS_FILE
     fi
     if [[ -d "active_plugins" ]]; then
-      echo "Installing CellProfiler-plugins requirements."
-      pip install -e . ${REQUIREMENTS} || (echo "Requirements install failed." & exit 1)
-      cd ..
+      (echo "Installing CellProfiler-plugins requirements." & pip install -e . ${REQUIREMENTS} & cd ..) || (echo "Requirements install failed." & exit 1)
     else 
-      echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements."
-      pip install -r ${REQUIREMENTS} || (echo "Requirements file not present or install failed; failing here." & exit 1)
-      cd ..
+      (echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements." & pip install -r ${REQUIREMENTS} & cd ..) || (echo "Requirements file not present or install failed; failing here." & exit 1)
     fi
   fi
 fi

From c89a343e8da280fbf91082cd48df08fbf7146d88 Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 22 Jan 2026 14:04:56 -0500
Subject: [PATCH 3/4] Double &

---
 worker/run-worker.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/worker/run-worker.sh b/worker/run-worker.sh
index 1226117..283c584 100644
--- a/worker/run-worker.sh
+++ b/worker/run-worker.sh
@@ -47,13 +47,13 @@ python3.8 instance-monitor.py &
 # 5. UPDATE AND/OR INSTALL PLUGINS
 if [[ ${USE_PLUGINS} == 'True' ]]; then
   if [[ ${UPDATE_PLUGINS} == 'True' ]]; then
-    (echo "Updating CellProfiler-plugins." & cd CellProfiler-plugins & git fetch --all & git pull & cd ..)
+    (echo "Updating CellProfiler-plugins." & cd CellProfiler-plugins && git fetch --all && git pull && cd ..)
   fi
   if [[ -z "$PLUGINS_COMMIT" ]]; then
     PLUGINS_COMMIT='False'
   fi
   if [[ ${PLUGINS_COMMIT} != 'False' ]]; then
-    (echo "Checking out specific CellProfiler-plugins commit." & cd CellProfiler-plugins & git checkout ${PLUGINS_COMMIT} & cd .. & echo "checkout successful" & sleep 3) || (echo "No such commit, branch, or version; failing here." & exit 1)
+    (echo "Checking out specific CellProfiler-plugins commit." & cd CellProfiler-plugins && git checkout ${PLUGINS_COMMIT} && cd .. && echo "checkout successful" && sleep 3) || (echo "No such commit, branch, or version; failing here." & exit 1)
   fi 
   if [[ ${INSTALL_REQUIREMENTS} == 'True' ]]; then
     cd CellProfiler-plugins
@@ -61,7 +61,7 @@ if [[ ${USE_PLUGINS} == 'True' ]]; then
       REQUIREMENTS = $REQUIREMENTS_FILE
     fi
     if [[ -d "active_plugins" ]]; then
-      (echo "Installing CellProfiler-plugins requirements." & pip install -e . ${REQUIREMENTS} & cd ..) || (echo "Requirements install failed." & exit 1)
+      (echo "Installing CellProfiler-plugins requirements." & pip install -e . ${REQUIREMENTS} && cd ..) || (echo "Requirements install failed." & exit 1)
     else 
       (echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements." & pip install -r ${REQUIREMENTS} & cd ..) || (echo "Requirements file not present or install failed; failing here." & exit 1)
     fi

From 0c8a4c11288316197ec2dcd9ccf07b99ec0b7d31 Mon Sep 17 00:00:00 2001
From: bethac07 <bcimini@broadinstitute.org>
Date: Thu, 22 Jan 2026 14:28:58 -0500
Subject: [PATCH 4/4] One more

---
 worker/run-worker.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/worker/run-worker.sh b/worker/run-worker.sh
index 283c584..02471c3 100644
--- a/worker/run-worker.sh
+++ b/worker/run-worker.sh
@@ -63,7 +63,7 @@ if [[ ${USE_PLUGINS} == 'True' ]]; then
     if [[ -d "active_plugins" ]]; then
       (echo "Installing CellProfiler-plugins requirements." & pip install -e . ${REQUIREMENTS} && cd ..) || (echo "Requirements install failed." & exit 1)
     else 
-      (echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements." & pip install -r ${REQUIREMENTS} & cd ..) || (echo "Requirements file not present or install failed; failing here." & exit 1)
+      (echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements." & pip install -r ${REQUIREMENTS} && cd ..) || (echo "Requirements file not present or install failed; failing here." & exit 1)
     fi
   fi
 fi