From bf31260192eede738e5e9e41b1cd1b490449333b Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sat, 1 Jun 2019 12:01:29 +0200 Subject: [PATCH] Call tool_script.sh with shell --- lib/galaxy/jobs/command_factory.py | 2 +- test/unit/jobs/test_command_factory.py | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py index ad99b0e1e56..db5cff813ce 100644 --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -140,7 +140,7 @@ def __externalize_commands(job_wrapper, shell, commands_builder, remote_command_ tool_commands ) write_script(local_container_script, script_contents, config) - commands = local_container_script + commands = "%s %s" % (shell, local_container_script) if 'working_directory' in remote_command_params: commands = "%s %s" % (shell, join(remote_command_params['working_directory'], script_name)) commands += " > ../tool_stdout 2> ../tool_stderr" diff --git a/test/unit/jobs/test_command_factory.py b/test/unit/jobs/test_command_factory.py index b5493c3698a..28f16c58f7b 100644 --- a/test/unit/jobs/test_command_factory.py +++ b/test/unit/jobs/test_command_factory.py @@ -45,7 +45,11 @@ class TestCommandFactory(TestCase): self.include_work_dir_outputs = False dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"] self.job_wrapper.dependency_shell_commands = dep_commands - self.__assert_command_is(_surround_command("%s/tool_script.sh > ../tool_stdout 2> ../tool_stderr; return_code=$?" % self.job_wrapper.working_directory)) + self.__assert_command_is(_surround_command( + "%s %s/tool_script.sh > ../tool_stdout 2> ../tool_stderr; return_code=$?" % ( + self.job_wrapper.shell, + self.job_wrapper.working_directory, + ))) self.__assert_tool_script_is("#!/bin/sh\n%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE)) def test_remote_dependency_resolution(self):