From 87eec325b934f5cbbc0b569037cb06b31187d015 Mon Sep 17 00:00:00 2001
From: Cedric Zhuang <jealous@163.com>
Date: Tue, 11 Jul 2023 15:59:52 +0800
Subject: [PATCH] [GH-32] Upload bin directory.

If the workflow contains a bin directory, upload to a tmp directory in
the working directory.

In `.command.run` script, we add `export PATH=...` to include the tmp
directory.
---
 .../nextflow/FloatGridExecutor.groovy         | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy b/plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy
index 069c43c..beea369 100644
--- a/plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy
+++ b/plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy
@@ -18,6 +18,7 @@ package com.memverge.nextflow
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.executor.AbstractGridExecutor
+import nextflow.extension.FilesEx
 import nextflow.processor.TaskConfig
 import nextflow.processor.TaskRun
 import nextflow.util.ServiceName
@@ -38,6 +39,8 @@ class FloatGridExecutor extends AbstractGridExecutor {
 
     private AtomicInteger serial = new AtomicInteger()
 
+    private String _binDir
+
     private FloatConf getFloatConf() {
         return FloatConf.getConf(session.config)
     }
@@ -49,6 +52,12 @@ class FloatGridExecutor extends AbstractGridExecutor {
         return _floatJobs
     }
 
+    @Override
+    protected void register() {
+        super.register()
+        uploadBinDir()
+    }
+
     @Override
     protected String getHeaderToken() {
         return ''
@@ -58,11 +67,32 @@ class FloatGridExecutor extends AbstractGridExecutor {
     protected List<String> getDirectives(TaskRun task, List<String> initial) {
         log.info "[float] switch task ${task.id} to ${task.workDirStr}"
         floatJobs.setWorkDir(task.id, task.workDirStr)
+
+        // go to the work directory
         initial << 'cd'
         initial << task.workDirStr
+
+        if (needBinDir()) {
+            // add path to the script
+            initial << 'export'
+            initial << 'PATH=$PATH:' + _binDir + '/bin'
+        }
         return initial
     }
 
+    private boolean needBinDir() {
+        return session.binDir && !session.binDir.empty() && !session.disableRemoteBinDir
+    }
+
+    private void uploadBinDir() {
+        // upload local binaries
+        if (needBinDir()) {
+            _binDir = getTempDir()
+            log.info "Uploading local `bin` ${session.binDir} to ${_binDir}/bin"
+            FilesEx.copyTo(session.binDir, _binDir)
+        }
+    }
+
     private void validateTaskConf(TaskConfig config) {
         if (!config.nfs && !floatConf.nfs) {
             log.error '[float] missing "nfs": need a nfs to run float jobs'