Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
comparison amplicon_analysis_pipeline.py @ 27:b5e43dfe07ac draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
author | pjbriggs |
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date | Fri, 28 Sep 2018 11:28:17 -0400 |
parents | f0917c340f13 |
children | 31b7950136ed |
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26:f0917c340f13 | 27:b5e43dfe07ac |
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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: |