ensemble: avoid JAVA_HOME overriding internal java #2778

bcbio · Apr 13, 2019 · 131cef1 · 131cef1
1 parent 14869f2
commit 131cef1
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/HISTORY.md b/HISTORY.md
@@ -1,3 +1,5 @@
+## 1.1.6 (in progress)
+
 ## 1.1.5 (12 April 2019)
 
 - Fixes for Python3 incompatibilities on distributed IPython runs.

diff --git a/bcbio/variation/ensemble.py b/bcbio/variation/ensemble.py
@@ -254,7 +254,7 @@ def _run_ensemble_intersection(batch_id, vrn_files, callers, base_dir, edata):
 
         with file_transaction(edata, out_vcf_file) as tx_out_file:
             cmd += [tx_out_file, dd.get_ref_file(edata)] + vrn_files
-            cmd = "%s %s" % (utils.local_path_export(), " ".join(str(x) for x in cmd))
+            cmd = "%s && %s" % (utils.get_java_clprep(), " ".join(str(x) for x in cmd))
             do.run(cmd, "Ensemble intersection calling: %s" % (batch_id))
     in_data = utils.deepish_copy(edata)
     in_data["vrn_file"] = out_vcf_file

diff --git a/setup.py b/setup.py
@@ -4,7 +4,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = "1.1.5"
+version = "1.1.6a"
 
 def write_version_py():
     version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline',