Fix CLI issues

build.gradle.kts

@@ -4,7 +4,7 @@ plugins {
 }
 
 group = "net.maizegenetics"
-version = "0.2.4"
+version = "0.2.5"
 
 repositories {
     mavenCentral()
@@ -19,7 +19,6 @@ dependencies {
     implementation("com.google.guava:guava:33.1.0-jre")
     implementation("com.github.samtools:htsjdk:4.0.1")
 
-
     testImplementation(kotlin("test"))
 }
 

src/main/kotlin/net/maizegenetics/commands/ConvertCoordinates.kt

@@ -111,8 +111,11 @@ class ConvertCoordinates : CliktCommand(name = "convert-coordinates") {
         }
 
         // Run convert_coords.py
+        // Set PYTHONPATH so Python can find the 'python' package for imports
+        val pythonPath = mlimputeDir.resolve("src").toString()
         logger.info("Running convert_coords.py")
         val exitCode = ProcessRunner.runCommand(
+            "env", "PYTHONPATH=$pythonPath",
             "pixi", "run",
             "python", pythonScript.toString(),
             "--assembly-list", assemblyList.toString(),

src/main/kotlin/net/maizegenetics/commands/GenerateRecombinedSequences.kt

@@ -120,8 +120,11 @@ class GenerateRecombinedSequences : CliktCommand(name = "generate-recombined-seq
         }
 
         // Run write_fastas.py
+        // Set PYTHONPATH so Python can find the 'python' package for imports
+        val pythonPath = mlimputeDir.resolve("src").toString()
         logger.info("Running write_fastas.py")
         val exitCode = ProcessRunner.runCommand(
+            "env", "PYTHONPATH=$pythonPath",
             "pixi", "run",
             "python", pythonScript.toString(),
             "--assembly-list", assemblyList.toString(),

src/main/kotlin/net/maizegenetics/commands/Orchestrate.kt

@@ -1,6 +1,7 @@
 package net.maizegenetics.commands
 
 import com.github.ajalt.clikt.core.CliktCommand
+import com.github.ajalt.clikt.core.parse
 import com.github.ajalt.clikt.parameters.options.default
 import com.github.ajalt.clikt.parameters.options.option
 import com.github.ajalt.clikt.parameters.options.required
@@ -167,24 +168,14 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
         logger.info("AUTO-SETUP: Running setup-environment")
         logger.info("=".repeat(80))
 
-        val args = buildList {
-            add("setup-environment")
-            add("--work-dir=${workDir}")
-        }
-
-        val exitCode = ProcessRunner.runCommand(
-            "./gradlew", "run", "--args=${args.joinToString(" ")}",
-            workingDir = File("."),
-            logger = logger
-        )
-
-        if (exitCode != 0) {
-            logger.error("setup-environment failed with exit code $exitCode")
-            return false
+        return try {
+            SetupEnvironment().parse(listOf("--work-dir=$workDir"))
+            logger.info("setup-environment completed successfully")
+            true
+        } catch (e: Exception) {
+            logger.error("setup-environment failed: ${e.message}", e)
+            false
         }
-
-        logger.info("setup-environment completed successfully")
-        return true
     }
 
     private fun parseYamlConfig(configPath: Path): PipelineConfig {
@@ -217,6 +208,7 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
             }
 
             // Parse maf_to_gvcf
+            @Suppress("UNCHECKED_CAST")
             val mafToGvcfMap = configMap["maf_to_gvcf"] as? Map<String, Any>
             val mafToGvcf = mafToGvcfMap?.let {
                 MafToGvcfConfig(
@@ -227,6 +219,7 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
             }
 
             // Parse downsample_gvcf
+            @Suppress("UNCHECKED_CAST")
             val downsampleGvcfMap = configMap["downsample_gvcf"] as? Map<String, Any>
             val downsampleGvcf = downsampleGvcfMap?.let {
                 DownsampleGvcfConfig(
@@ -241,6 +234,7 @@ class Orchestrate : CliktCommand(name = "orchestrate") {
             }
 
             // Parse convert_to_fasta
+            @Suppress("UNCHECKED_CAST")
             val convertToFastaMap = configMap["convert_to_fasta"] as? Map<String, Any>
             val convertToFasta = convertToFastaMap?.let {
                 ConvertToFastaConfig(

src/main/kotlin/net/maizegenetics/commands/PickCrossovers.kt

@@ -77,12 +77,17 @@ class PickCrossovers : CliktCommand(name = "pick-crossovers") {
         FileUtils.createOutputDirectory(outputDir, logger)
 
         // Run pick_crossovers.py
+        // Set PYTHONPATH so Python can find the 'python' package for imports
+        // Use absolute paths since the working directory is set to outputDir
+        // Use sh -c to set PYTHONPATH inside pixi's environment
+        val pythonPath = mlimputeDir.resolve("src").toAbsolutePath().toString()
+        val scriptPath = pythonScript.toAbsolutePath().toString()
+        val refFastaPath = refFasta.toAbsolutePath().toString()
+        val assemblyListPath = assemblyList.toAbsolutePath().toString()
+        val shellCommand = "PYTHONPATH='$pythonPath' python '$scriptPath' --ref-fasta '$refFastaPath' --assembly-list '$assemblyListPath'"
         logger.info("Running pick_crossovers.py")
         val exitCode = ProcessRunner.runCommand(
-            "pixi", "run",
-            "python", pythonScript.toString(),
-            "--ref-fasta", refFasta.toString(),
-            "--assembly-list", assemblyList.toString(),
+            "pixi", "run", "sh", "-c", shellCommand,
             workingDir = outputDir.toFile(),
             logger = logger
         )

src/main/kotlin/net/maizegenetics/commands/SetupEnvironment.kt

@@ -98,7 +98,8 @@ class SetupEnvironment : CliktCommand(name = "setup-environment") {
             .toFile()
 
         if (mlImputeGradlew.exists()) {
-            if (mlImputeGradlew.setExecutable(true)) {
+            // setExecutable(true, false) makes it executable for all users (like chmod +x)
+            if (mlImputeGradlew.setExecutable(true, false)) {
                 logger.info("Made MLImpute gradlew executable: ${mlImputeGradlew.path}")
             } else {
                 logger.warn("Failed to set executable permissions on gradlew: ${mlImputeGradlew.path}")

src/main/resources/pixi.toml

@@ -20,6 +20,7 @@ seqkit = "*"
 crossmap = "*"
 parallel = "*"
 pysam = "*"
+samtools = "*"
 
 # Linux-only dependencies (AnchorWave not available on macOS)
 [target.linux-64.dependencies]