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Fix command line for tools using interpreter when galaxy root contains spaces

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This commit is contained in:
Nicola Soranzo
2020-11-10 19:29:22 +00:00
parent 1e9f83b53e
commit efa9e0fdd1
1 changed files with 5 additions and 3 deletions
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lib/galaxy/tools/evaluation.py
+5 -3
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@@ -1,6 +1,7 @@
import json
import logging
import os
import shlex
import tempfile
@@ -494,11 +495,12 @@ class ToolEvaluator:
raise
if interpreter:
# TODO: path munging for cluster/dataset server relocatability
executable = command_line.split()[0]
command_line_tokens = shlex.split(command_line)
executable = command_line_tokens[0]
tool_dir = os.path.abspath(self.tool.tool_dir)
abs_executable = os.path.join(tool_dir, executable)
command_line = command_line.replace(executable, abs_executable, 1)
command_line = interpreter + " " + command_line
command_line_tokens[0:1] = [interpreter, abs_executable]
command_line = ' '.join(map(shlex.quote, command_line_tokens))
self.command_line = command_line
def __build_config_files(self):