Mercurial > repos > trinity_ctat > align_and_estimate_abundance

changeset 11:2e0e45063fad draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Trying to fix a syntax error. Seems like the wrong python is being used.
author trinity_ctat
date Tue, 26 Sep 2017 22:56:18 -0400
parents a8fa525a2f30
children a130d5b5f34b
files align_and_estimate_abundance.xml trinityToolWrapper.py
diffstat 2 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/align_and_estimate_abundance.xml	Tue Sep 26 22:26:13 2017 -0400
+++ b/align_and_estimate_abundance.xml	Tue Sep 26 22:56:18 2017 -0400
@@ -10,9 +10,9 @@
         <requirement type="package">rsem</requirement>
     </requirements>
 
-    <command interpreter="python">
+    <command>
         <![CDATA[
-        trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir  "subdir" 
+        python trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir  "subdir" 
 
         ## Inputs.
         #if str($inputs.paired_or_single) == "paired":
--- a/trinityToolWrapper.py	Tue Sep 26 22:26:13 2017 -0400
+++ b/trinityToolWrapper.py	Tue Sep 26 22:56:18 2017 -0400
@@ -10,6 +10,7 @@
 """
 
 import sys, subprocess, os
+print sys.version
 
 assert sys.version_info[:2] >= ( 2, 4 )