Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 142:b36f12eb99dc draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 17 Apr 2021 12:29:31 +0000 |
| parents | 6b414af9ca11 |
| children | 4de39d209c5b |
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| 141:b7b0c4527460 | 142:b36f12eb99dc |
|---|---|
| 1041 """planemo is a requirement so is available for testing but needs a | 1041 """planemo is a requirement so is available for testing but needs a |
| 1042 different call if in the biocontainer - see above | 1042 different call if in the biocontainer - see above |
| 1043 and for generating test outputs if command or test overrides are | 1043 and for generating test outputs if command or test overrides are |
| 1044 supplied test outputs are sent to repdir for display | 1044 supplied test outputs are sent to repdir for display |
| 1045 """ | 1045 """ |
| 1046 penv = os.environ | |
| 1047 pconfig = os.path.join(self.args.tool_dir, '.planemo.yml') | |
| 1048 penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig | |
| 1049 self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig) | |
| 1050 xreal = "%s.xml" % self.tool_name | 1046 xreal = "%s.xml" % self.tool_name |
| 1051 tool_test_path = os.path.join( | 1047 tool_test_path = os.path.join( |
| 1052 self.repdir, f"{self.tool_name}_planemo_test_report.html" | 1048 self.repdir, f"{self.tool_name}_planemo_test_report.html" |
| 1053 ) | 1049 ) |
| 1054 if os.path.exists(self.tlog): | 1050 if os.path.exists(self.tlog): |
| 1071 os.path.abspath(xreal), | 1067 os.path.abspath(xreal), |
| 1072 ] | 1068 ] |
| 1073 p = subprocess.run( | 1069 p = subprocess.run( |
| 1074 cll, | 1070 cll, |
| 1075 shell=False, | 1071 shell=False, |
| 1076 env=penv, | |
| 1077 cwd=self.tooloutdir, | 1072 cwd=self.tooloutdir, |
| 1078 stderr=tout, | 1073 stderr=tout, |
| 1079 stdout=tout, | 1074 stdout=tout, |
| 1080 ) | 1075 ) |
| 1081 tout.close() | 1076 tout.close() |