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Fix command line building when using interpreter

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Partially revert commit efa9e0fdd1
which broke tools which use `interpreter` and `&&` or environment
variables in the `<command />`.

xref.: https://github.com/galaxyproject/galaxy/pull/10674/commits/efa9e0fdd1d11d58f4a504a3e8242cc59f3f1416#r573844945
This commit is contained in:
Nicola Soranzo
2021-02-10 18:33:12 +00:00
parent 0bbd883ad8
commit 766e96e417
1 changed files with 2 additions and 4 deletions
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lib/galaxy/tools/evaluation.py
+2 -4
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@@ -495,12 +495,10 @@ class ToolEvaluator:
raise
if interpreter:
# TODO: path munging for cluster/dataset server relocatability
command_line_tokens = shlex.split(command_line)
executable = command_line_tokens[0]
executable = command_line.split()[0]
tool_dir = os.path.abspath(self.tool.tool_dir)
abs_executable = os.path.join(tool_dir, executable)
command_line_tokens[0:1] = [interpreter, abs_executable]
command_line = ' '.join(map(shlex.quote, command_line_tokens))
command_line = command_line.replace(executable, f"{interpreter} {shlex.quote(abs_executable)}", 1)
self.command_line = command_line
def __build_config_files(self):