Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison amplicon_analysis_pipeline.py @ 24:fe354f5dd0ee draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
author pjbriggs
date Thu, 30 Aug 2018 08:13:55 -0400
parents eb7d118dd322
children fd65832d1074
comparison
equal deleted inserted replaced
23:545f23776953 24:fe354f5dd0ee
232 qiime_config.write("qiime_scripts_dir\t%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 # Check for fasta_number.py
238 fasta_number = find_executable("fasta_number.py")
239 if not fasta_number:
240 # Make a link to relabel_fasta.py
241 relabel_fasta_path = os.path.join(os.path.realpath(__file__),
242 "relabel_fasta.py")
243 fasta_number_path = os.path.join(os.path.abspath("bin"),
244 "fasta_number.py")
245 os.symlink(relabel_fasta_path,fasta_number_path)
237 246
238 # Construct the pipeline command 247 # Construct the pipeline command
239 print "Amplicon analysis: constructing pipeline command" 248 print "Amplicon analysis: constructing pipeline command"
240 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh") 249 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
241 if args.forward_pcr_primer: 250 if args.forward_pcr_primer: