add local singularity image parameter

weng-lab · Oct 23, 2023 · 33cf281 · 33cf281
1 parent d6d11b8
commit 33cf281
Show file tree

Hide file tree

Showing 4 changed files with 14 additions and 5 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -13,7 +13,7 @@ plugins {
 }
 
 group = "io.krews"
-version = "0.14.15"
+version = "0.15.0"
 
 repositories {
     maven { setUrl("https://dl.bintray.com/kotlin/kotlin-eap") }

diff --git a/src/main/kotlin/krews/config/BaseConfig.kt b/src/main/kotlin/krews/config/BaseConfig.kt
@@ -1,5 +1,9 @@
 package krews.config
 
+data class SingularityConfig (
+    val localImage: String? = null
+)
+
 data class TaskConfig (
     // Task level input parameters
     val params: Map<String, Any> = mapOf(),
@@ -14,7 +18,9 @@ data class TaskConfig (
     // The number of tasks "executions" that will be run with the same job / vm.
     val grouping: Int = 1,
     // Docker image; defaults to one provided by task
-    val dockerImage: String? = null
+    val dockerImage: String? = null,
+    // optional Singularity config
+    val singularity: SingularityConfig? = null
 )
 
 data class WorkflowConfig (

diff --git a/src/main/kotlin/krews/executor/bsub/BsubExecutor.kt b/src/main/kotlin/krews/executor/bsub/BsubExecutor.kt
@@ -191,10 +191,11 @@ class BsubExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirected
             bsubScript.append("export SINGULARITY_BIND=\"$binds\"\n")
 
             // Add running the task to script
-            val remoteImage = !taskRunContext.dockerImage.endsWith(".sif")
+            val trueImage = taskConfig.singularity?.localImage ?: taskRunContext.dockerImage
+            val remoteImage = !trueImage.endsWith(".sif")
             bsubScript.append("\n")
             bsubScript.append("# Run task command.\n")
-            bsubScript.append("singularity exec --containall ${if (remoteImage) "docker://" else ""}${taskRunContext.dockerImage} $containerCommand")
+            bsubScript.append("singularity exec --containall ${if (remoteImage) "docker://" else ""}${trueImage} $containerCommand")
             bsubScript.append("\n")
 
             // Add copying output files into output dir to script

diff --git a/src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt b/src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt
@@ -195,9 +195,11 @@ class SlurmExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirecte
             sbatchScript.append("export SINGULARITY_BIND=\"$binds\"\n")
 
             // Add running the task to script
+            val trueImage = taskConfig.singularity?.localImage ?: taskRunContext.dockerImage
+            val remoteImage = !trueImage.endsWith(".sif")
             sbatchScript.append("\n")
             sbatchScript.append("# Run task command.\n")
-            sbatchScript.append("singularity exec --containall docker://${taskRunContext.dockerImage} $containerCommand")
+            sbatchScript.append("singularity exec --containall ${if (remoteImage) "docker://" else ""}${trueImage} $containerCommand")
             sbatchScript.append("\n")
 
             // Add copying output files into output dir to script