comparison amplicon_analysis_pipeline.py @ 27:b5e43dfe07ac draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
author pjbriggs
date Fri, 28 Sep 2018 11:28:17 -0400
parents f0917c340f13
children 31b7950136ed
comparison
equal deleted inserted replaced
26:f0917c340f13 27:b5e43dfe07ac
188 fasta_splitter = find_executable("fasta-splitter.pl") 188 fasta_splitter = find_executable("fasta-splitter.pl")
189 if fasta_splitter is None: 189 if fasta_splitter is None:
190 fasta_splitter = os.readlink( 190 fasta_splitter = os.readlink(
191 find_executable("fasta-splitter")) 191 find_executable("fasta-splitter"))
192 if fasta_splitter: 192 if fasta_splitter:
193 os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl")) 193 os.symlink(fasta_splitter,os.path.join("bin","fasta-splitter.pl"))
194 print "-- made symlink to %s" % fasta_splitter 194 print "-- made symlink to %s" % fasta_splitter
195 else: 195 else:
196 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n") 196 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")
197 # Qiime 1.8.0 wants 'RDP_JAR_PATH' env var to point to 197 # Qiime 1.8.0 wants 'RDP_JAR_PATH' env var to point to
198 # the rdp_classifier.jar file 198 # the rdp_classifier.jar file
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.dirname(__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)
246 print "-- linked %s to %s" % (relabel_fasta_path,
247 fasta_number_path)
248 237
249 # Construct the pipeline command 238 # Construct the pipeline command
250 print "Amplicon analysis: constructing pipeline command" 239 print "Amplicon analysis: constructing pipeline command"
251 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh") 240 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
252 if args.forward_pcr_primer: 241 if args.forward_pcr_primer: