Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

diff amplicon_analysis_pipeline.py @ 24:fe354f5dd0ee draft

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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
line wrap: on
line diff
--- a/amplicon_analysis_pipeline.py	Wed Aug 29 10:57:51 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Thu Aug 30 08:13:55 2018 -0400
@@ -234,6 +234,15 @@
                                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.realpath(__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)
 
     # Construct the pipeline command
     print "Amplicon analysis: constructing pipeline command"