From 3dcdad9eba31bf1b689f9bfb2e95908f8c4c2c55 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 27 Jan 2017 08:12:14 -0500
Subject: [PATCH] Add sam_to_bam to list of tools requiring Galaxy's
 environment.

Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj.
---
 lib/galaxy/tools/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c7fe3330b42..36e0afaa29f 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -133,6 +133,7 @@ GALAXY_LIB_TOOLS = [
     "sam_pileup",
     "find_diag_hits",
     "cufflinks",
+    "sam_to_bam",  # This was fixed with version 1.1.3 of the tool - TODO add Galaxy to PYTHONPATH only for older versions
     # Tools improperly migrated to the tool shed (iuc)
     "tabular_to_dbnsfp",
 ]