Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

changeset 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 b355098dc1f6
children 18e6427c5e4a
files amplicon_analysis_pipeline.py
diffstat 1 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/amplicon_analysis_pipeline.py	Mon Oct 01 05:10:52 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Mon Oct 01 07:31:44 2018 -0400
@@ -99,7 +99,9 @@
 def find_executable(name):
     # Locate executable on PATH
     for p in os.environ['PATH'].split(os.pathsep):
-        exe = os.path.join(p,name)
+        exe = os.path.normpath(
+            os.path.abspath(os.path.join(p,name)))
+        print "Checking %s" % exe
         if os.path.isfile(exe) and os.access(exe,os.X_OK):
             return exe
     return None
@@ -187,8 +189,11 @@
     # 'fasta-splitter'
     fasta_splitter = find_executable("fasta-splitter.pl")
     if fasta_splitter is None:
-        fasta_splitter = os.readlink(
-            find_executable("fasta-splitter"))
+        fasta_splitter = find_executable("fasta-splitter")
+        if os.path.islink(fasta_splitter):
+            fasta_splitter = os.path.join(
+                os.path.dirname(fasta_splitter),
+                os.readlink(fasta_splitter))
     if fasta_splitter:
         os.symlink(fasta_splitter,os.path.join("bin","fasta-splitter.pl"))
         print "-- made symlink to %s" % fasta_splitter