[FLOAT-4537] Failed to execute user binary.

When we update the LD_LIBRARY_PATH, it may also affect the user executables. So instead of updating the environment variable, use a function to redirect the call to our aws cli when it is not found in the path.
MemVerge · Sep 25, 2024 · 9784a20 · 9784a20
1 parent cce3f14
commit 9784a20
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Showing 3 changed files with 14 additions and 13 deletions.
diff --git a/plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy b/plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy
@@ -131,8 +131,13 @@ class FloatGridExecutor extends AbstractGridExecutor {
         if (floatConf.s3cred.isValid()) {
             // if we have s3 credential, make sure aws cli is available in path
             result += floatConf.s3cred.getExportS3CredScript(getRunName())
-            result += "export PATH=\$PATH:/opt/aws/dist\n"
-            result += "export LD_LIBRARY_PATH=\$LIBRARY_PATH:/opt/aws/dist\n"
+            result += '''
+if ! command -v aws >/dev/null 2>&1 && ! type aws >/dev/null 2>&1; then
+    aws() {
+        LD_LIBRARY_PATH=/opt/aws/dist:\$LD_LIBRARY_PATH /opt/aws/dist/aws \$@
+    }
+fi
+'''
         }
         return result
     }

diff --git a/plugins/nf-float/src/resources/META-INF/MANIFEST.MF b/plugins/nf-float/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: com.memverge.nextflow.FloatPlugin
 Plugin-Id: nf-float
-Plugin-Version: 0.4.5
+Plugin-Version: 0.4.6
 Plugin-Provider: MemVerge Corp.
 Plugin-Requires: >=23.04.0
diff --git a/plugins/nf-float/src/test/com/memverge/nextflow/GlobalTest.groovy b/plugins/nf-float/src/test/com/memverge/nextflow/GlobalTest.groovy
@@ -1,9 +1,5 @@
 package com.memverge.nextflow
 
-import nextflow.processor.TaskConfig
-
-import java.nio.file.Paths
-
 class GlobalTest extends FloatBaseTest {
     def "get env var. of any names"() {
         given:
@@ -68,7 +64,7 @@ class GlobalTest extends FloatBaseTest {
         given:
         setEnv("AWS_ACCESS_KEY", "A")
         setEnv("AWS_SECRET_KEY", "B")
-        def config = [aws:[]]
+        def config = [aws: []]
 
         when:
         def res = Global.getAwsCredentials(config)
@@ -97,7 +93,7 @@ class GlobalTest extends FloatBaseTest {
     def "retrieve aws credentials from system env, with token"() {
         given:
         setAwsEnvs()
-        def config = [aws:[]]
+        def config = [aws: []]
 
         when:
         def res = Global.getAwsCredentials(config)
@@ -114,11 +110,11 @@ class GlobalTest extends FloatBaseTest {
     def "update arg map with aws credential"() {
         given:
         setAwsEnvs()
-        def config = [aws:[]]
+        def config = [aws: []]
 
         when:
         def res = Global.getAwsCredentials(config)
-        def argMap = res.updateMap(['banana':'apple'])
+        def argMap = res.updateMap(['banana': 'apple'])
 
         then:
         res.isValid() == true
@@ -134,7 +130,7 @@ class GlobalTest extends FloatBaseTest {
     def "update env map with aws credential"() {
         given:
         setAwsEnvs()
-        def config = [aws:[]]
+        def config = [aws: []]
 
         when:
         def res = Global.getAwsCredentials(config)
@@ -160,7 +156,7 @@ class GlobalTest extends FloatBaseTest {
         def script = exec.getHeaderScript(task)
 
         then:
-        script.contains("PATH:/opt/aws/dist")
+        script.contains('/opt/aws/dist:$LD_LIBRARY_PATH')
 
         cleanup:
         clearAwsEnvs()