Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Default to running Python 3
--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
+++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
+++ trinityrnaseq/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
+++ trinityrnaseq/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division, print_function, unicode_literals)
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/DP_matrix.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/DP_matrix.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/GraphCycleException.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/GraphCycleException.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Node_alignment.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_alignment.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Node_path.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_path.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TGLOBALS.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 DEBUG = False
 
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TGraph.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TGraph.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TNode.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TNode.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Topological_sort.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Topological_sort.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Trinity_util.py
+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_util.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/PyLib/Pipeliner.py
+++ trinityrnaseq/PyLib/Pipeliner.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
+++ trinityrnaseq/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
+++ trinityrnaseq/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys, collections, itertools, os.path, optparse
 
--- trinityrnaseq.orig/util/misc/TPM_weighted_gene_length.py
+++ trinityrnaseq/util/misc/TPM_weighted_gene_length.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # encoding: utf-8
 
 from __future__ import (absolute_import, division,
--- trinityrnaseq.orig/util/support_scripts/trinity_installer.py
+++ trinityrnaseq/util/support_scripts/trinity_installer.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os, re, sys, subprocess
 
