diff amplicon_analysis_pipeline.py @ 27:b5e43dfe07ac draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979

--- a/amplicon_analysis_pipeline.py	Thu Aug 30 08:41:11 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Fri Sep 28 11:28:17 2018 -0400
@@ -190,7 +190,7 @@
         fasta_splitter = os.readlink(
             find_executable("fasta-splitter"))
     if fasta_splitter:
-        os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
+        os.symlink(fasta_splitter,os.path.join("bin","fasta-splitter.pl"))
         print "-- made symlink to %s" % fasta_splitter
     else:
         sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")
@@ -234,17 +234,6 @@
                                find_executable("single_rarefaction.py")))
     os.environ["QIIME_CONFIG_FP"] = qiime_config_file
     print "-- set QIIME_CONFIG_FP: %s" % os.environ["QIIME_CONFIG_FP"]
-    # Check for fasta_number.py
-    fasta_number = find_executable("fasta_number.py")
-    if not fasta_number:
-        # Make a link to relabel_fasta.py
-        relabel_fasta_path = os.path.join(os.path.dirname(__file__),
-                                          "relabel_fasta.py")
-        fasta_number_path = os.path.join(os.path.abspath("bin"),
-                                         "fasta_number.py")
-        os.symlink(relabel_fasta_path,fasta_number_path)
-        print "-- linked %s to %s" % (relabel_fasta_path,
-                                      fasta_number_path)
 
     # Construct the pipeline command
     print "Amplicon analysis: constructing pipeline command"