Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison amplicon_analysis_pipeline.py @ 22:eb7d118dd322 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit bae32168fbfd40305a4768b889a8e7689e5987e3-dirty
author pjbriggs
date Wed, 04 Jul 2018 06:56:48 -0400
parents 092e39db5f59
children fe354f5dd0ee
comparison
equal deleted inserted replaced
21:092e39db5f59 22:eb7d118dd322
227 sys.stderr.write("Missing 'rdp_classifier.jar'\n") 227 sys.stderr.write("Missing 'rdp_classifier.jar'\n")
228 # Set up qiime_config file 228 # Set up qiime_config file
229 qiime_config_file = os.path.abspath("qiime_config") 229 qiime_config_file = os.path.abspath("qiime_config")
230 with open(qiime_config_file,'w') as qiime_config: 230 with open(qiime_config_file,'w') as qiime_config:
231 # Set qiime_scripts_dir 231 # Set qiime_scripts_dir
232 qiime_config.write("qiime_scripts_dir: %s" % 232 qiime_config.write("qiime_scripts_dir\t%s" %
233 os.path.dirname( 233 os.path.dirname(
234 find_executable("single_rarefaction.py"))) 234 find_executable("single_rarefaction.py")))
235 os.environ["QIIME_CONFIG_FP"] = qiime_config_file 235 os.environ["QIIME_CONFIG_FP"] = qiime_config_file
236 print "-- set QIIME_CONFIG_FP: %s" % os.environ["QIIME_CONFIG_FP"] 236 print "-- set QIIME_CONFIG_FP: %s" % os.environ["QIIME_CONFIG_FP"]
237 237