Commit 653760d4 authored by mmanno's avatar mmanno
Browse files

Change path to scripts R

parent 278939c7
......@@ -300,7 +300,7 @@ class Utils(object):
"""
group_basenames = {}
for file in file_list:
for file in file_list:
file_name_fields = os.path.basename(file).split(Utils.CASAVA_FILENAME_SEPARATOR)
group_tag = Utils.CASAVA_FILENAME_SEPARATOR.join( file_name_fields[:Utils.CASAVA_FILENAME[group_by]] )
......@@ -309,7 +309,7 @@ class Utils(object):
group_basenames[group_tag].append(file)
else:
group_basenames[group_tag] = [file]
logging.getLogger("Utils").debug("get_group_basenames. group_basenames = " + ",".join(group_basenames))
return group_basenames
@staticmethod
......
......@@ -227,14 +227,14 @@ class Run_stats (Analysis):
#print (self.sequencing_summary_file)
self.add_shell_execution(self.get_exec_path("Rscript") +" /work/ng6-test/claire/test_ont_qc/graph_albacoresummary.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2',
self.add_shell_execution(self.get_exec_path("Rscript") +" /save/sbsuser/scripts-ngs/current/ont/graph_albacoresummary.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2',
cmd_format='{EXE} {IN} {OUT}' ,
map=False,
inputs = self.sequencing_summary_file,
outputs = self.stderr)
if self.barcoded == "yes" :
self.add_shell_execution(self.get_exec_path("Rscript") +" /work/ng6-test/claire/test_ont_qc/graph_albacoresummary_barcode.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2',
self.add_shell_execution(self.get_exec_path("Rscript") +" /save/sbsuser/scripts-ngs/current/ont/graph_albacoresummary_barcode.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2',
cmd_format='{EXE} {IN} {OUT}' ,
map=False,
inputs = self.sequencing_summary_file,
......
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