Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison amplicon_analysis_pipeline.py @ 29:31b7950136ed draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit afee03cb577aa68e650a2b7d65b31c000440d9ee
author pjbriggs
date Mon, 01 Oct 2018 07:31:44 -0400
parents b5e43dfe07ac
children 18e6427c5e4a
comparison
equal deleted inserted replaced
28:b355098dc1f6 29:31b7950136ed
97 fp.close() 97 fp.close()
98 98
99 def find_executable(name): 99 def find_executable(name):
100 # Locate executable on PATH 100 # Locate executable on PATH
101 for p in os.environ['PATH'].split(os.pathsep): 101 for p in os.environ['PATH'].split(os.pathsep):
102 exe = os.path.join(p,name) 102 exe = os.path.normpath(
103 os.path.abspath(os.path.join(p,name)))
104 print "Checking %s" % exe
103 if os.path.isfile(exe) and os.access(exe,os.X_OK): 105 if os.path.isfile(exe) and os.access(exe,os.X_OK):
104 return exe 106 return exe
105 return None 107 return None
106 108
107 if __name__ == "__main__": 109 if __name__ == "__main__":
185 sys.stderr.write("Missing 'vsearch[113]'\n") 187 sys.stderr.write("Missing 'vsearch[113]'\n")
186 # Pipeline wants 'fasta-splitter.pl' but bioconda provides 188 # Pipeline wants 'fasta-splitter.pl' but bioconda provides
187 # 'fasta-splitter' 189 # 'fasta-splitter'
188 fasta_splitter = find_executable("fasta-splitter.pl") 190 fasta_splitter = find_executable("fasta-splitter.pl")
189 if fasta_splitter is None: 191 if fasta_splitter is None:
190 fasta_splitter = os.readlink( 192 fasta_splitter = find_executable("fasta-splitter")
191 find_executable("fasta-splitter")) 193 if os.path.islink(fasta_splitter):
194 fasta_splitter = os.path.join(
195 os.path.dirname(fasta_splitter),
196 os.readlink(fasta_splitter))
192 if fasta_splitter: 197 if fasta_splitter:
193 os.symlink(fasta_splitter,os.path.join("bin","fasta-splitter.pl")) 198 os.symlink(fasta_splitter,os.path.join("bin","fasta-splitter.pl"))
194 print "-- made symlink to %s" % fasta_splitter 199 print "-- made symlink to %s" % fasta_splitter
195 else: 200 else:
196 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n") 201 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")