Fix direct write to service account directories

core/modes/__init__.py

@@ -404,14 +404,25 @@ class Batch(Slurm):
 class Singularity_Batch(Default):
     container = ''
 
+    @staticmethod
+    def escape(s):
+        return s.replace('/', '\/')
+
     def custom_run_setup(self, **kwargs):
         Sbatch.custom_run_setup(self, **kwargs)
         if kwargs["script_execution"] and kwargs["do_inbetween_processing"]:
             logging.debug('Creating param file')
             # write env_file
-            with open(f'{self.slurm_output_dir}/env{self.job.jobid}', 'w') as file:
+            with open(f'{self.job.tmp_dir}/env{self.job.jobid}', 'w') as file:
                 file.write(f"CONTAINER={self.container}\0EXEC_WRAPPER={srun_path}\0PARAMS={self.job.get_parameters()}\0OUTPUT_FILE=--output={self.slurm_output_file}")
 
+
+            self.job.execute(f'/usr/bin/cp /dev/stdin '
+                             f'{self.slurm_output_dir}/batchEnv{self.job.jobid}',
+                             f"{self.job.tmp_dir}/env{self.job.jobid}",
+                             f"{self.job.driver_path}/core/scripts/pipeHelper.sh",
+                             skip_env=True, srun_wrap=True)
+
     def get_combiner_script(self):
         self._combiner_script = f"{self.job.driver_path}/core/scripts/pipeHelper.sh"
         return self._combiner_script
@@ -445,7 +456,7 @@ class Singularity_Batch(Default):
                          skip_env=True, srun_wrap=True)
         # add singularity specific parameter to the properties
         property_split = self._run_properties.split(" ")
-        property_split.insert(1, f'--export-file={self.slurm_output_dir}/env{self.job.jobid}')
+        property_split.insert(1, f'--export-file={self.slurm_output_dir}/batchEnv{self.job.jobid}')
         self._run_properties = " ".join(property_split)
         return self._run_properties
 

core/scripts/batch.env

+CONTAINER=_CONTAINER\0EXEC_WRAPPER=_EXEC_WRAPPER\0PARAMS=_PARAMS\0OUTPUT_FILE=_OUTPUT_FILE

core/scripts/chmodPath.sh

@@ -2,7 +2,7 @@
 _path=$1
 set -e
 while test "$_path" != "/work"; do
-    chmod o+wx "$_path"
+    chmod o+x "$_path"
     _path=$(dirname "$_path")
 done