Mercurial > repos > devteam > data_manager_picard_index_builder

changeset 4:99847f7b3a32 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 59ee07d9786f1a090053b4a13192247872389d61
author iuc
date Mon, 10 Apr 2017 06:06:09 -0400
parents 0663d25e619c
children acaa6719a478
files data_manager/picard_index_builder.py
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/picard_index_builder.py	Tue Apr 04 17:52:40 2017 -0400
+++ b/data_manager/picard_index_builder.py	Mon Apr 10 06:06:09 2017 -0400
@@ -31,7 +31,7 @@
     prefix = os.path.splitext( fasta_base_name )[0]
     sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
     os.symlink( fasta_filename, sym_linked_fasta_filename )
-    args = [ 'java', '-Xmx4G', '-jar', os.path.join( os.environ[ 'JAVA_JAR_PATH' ], 'CreateSequenceDictionary.jar' ), 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ]
+    args = [ 'picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
     if return_code: