Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
comparison amplicon_analysis_pipeline.py @ 24:fe354f5dd0ee draft
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 |
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| 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: |