Commit 6e272c00 authored by Gerald Salin's avatar Gerald Salin
Browse files

bug in python >2, add get_exec_path(python3) to get the version to be

used from the application.properties
parent 0a0fcc3f
......@@ -165,11 +165,11 @@ class AlignmentStats (Analysis):
# Alignment quality stats
if self.csv_files_r2:
self.add_shell_execution(self.get_exec_path("samtools") + " view -F0x0100 $1 | python " + self.get_exec_path("cigarlineGraph.py") + " -i - -t $2 $3 " + self.cigar_options + " 2> $4",
self.add_shell_execution(self.get_exec_path("samtools") + " view -F0x0100 $1 | " + self.get_exec_path("python3") + " " + self.get_exec_path("cigarlineGraph.py") + " -i - -t $2 $3 " + self.cigar_options + " 2> $4",
cmd_format='{EXE} {IN} {OUT}', map=True,
inputs=self.bam_files, outputs=[self.csv_files_r1, self.csv_files_r2, self.cigar_stderrs])
else:
self.add_shell_execution(self.get_exec_path("samtools") + " view -F0x0100 $1 | python " + self.get_exec_path("cigarlineGraph.py") + " -i - -t $2 " + self.cigar_options + " 2> $3",
self.add_shell_execution(self.get_exec_path("samtools") + " view -F0x0100 $1 | " + self.get_exec_path("python3") + " " + self.get_exec_path("cigarlineGraph.py") + " -i - -t $2 " + self.cigar_options + " 2> $3",
cmd_format='{EXE} {IN} {OUT}', map=True,
inputs=self.bam_files, outputs=[self.csv_files_r1, self.cigar_stderrs])
......
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