From d21fb3c5e184540fd2e494056a4e4669f2f31027 Mon Sep 17 00:00:00 2001
From: labkey-tchad <tchad@labkey.com>
Date: Thu, 9 Jan 2025 09:58:03 -0800
Subject: [PATCH 1/2] Revert "Fix JBrowseTest (#330)"

This reverts commit 0728b90c0a7ed52f6d81df5c48fd0c00e270db78.
---
 .../api/sequenceanalysis/run/AbstractCommandWrapper.java     | 5 -----
 SequenceAnalysis/test/configs/pipelineConfig.xml             | 5 -----
 2 files changed, 10 deletions(-)

diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
index e9b0df727..2e3e84e2c 100644
--- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
+++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
@@ -204,11 +204,6 @@ private void setPath(ProcessBuilder pb)
         if (!StringUtils.isEmpty(toolDir))
         {
             String path = System.getenv("PATH");
-
-            getLogger().debug("Existing PATH: " + path);
-            getLogger().debug("toolDir: " + toolDir);
-
-
             if (path == null)
             {
                 path = toolDir;
diff --git a/SequenceAnalysis/test/configs/pipelineConfig.xml b/SequenceAnalysis/test/configs/pipelineConfig.xml
index 4279c2acb..febf454b1 100644
--- a/SequenceAnalysis/test/configs/pipelineConfig.xml
+++ b/SequenceAnalysis/test/configs/pipelineConfig.xml
@@ -4,11 +4,6 @@
        xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd">
 
     <bean id="pipelineJobService" class="org.labkey.pipeline.api.PipelineJobServiceImpl">
-        <property name="appProperties">
-            <bean class="org.labkey.pipeline.api.properties.ApplicationPropertiesImpl">
-                <property name="toolsDirectory" value="@@SEQUENCEANALYSIS_TOOLS@@" />
-            </bean>
-        </property>
         <property name="configProperties">
             <bean class="org.labkey.pipeline.api.properties.ConfigPropertiesImpl">
                 <property name="softwarePackages">

From f428678156f176303d2a257eddd55e2e86d2c0eb Mon Sep 17 00:00:00 2001
From: labkey-tchad <tchad@labkey.com>
Date: Thu, 9 Jan 2025 10:45:43 -0800
Subject: [PATCH 2/2] Re-add logging

---
 .../api/sequenceanalysis/run/AbstractCommandWrapper.java     | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
index 2e3e84e2c..e9b0df727 100644
--- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
+++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
@@ -204,6 +204,11 @@ private void setPath(ProcessBuilder pb)
         if (!StringUtils.isEmpty(toolDir))
         {
             String path = System.getenv("PATH");
+
+            getLogger().debug("Existing PATH: " + path);
+            getLogger().debug("toolDir: " + toolDir);
+
+
             if (path == null)
             {
                 path = toolDir;