Commit 55d9d0d8 authored by Gerald Salin's avatar Gerald Salin
Browse files

re-add --pat_to_bowtie, because the instance in the path pointed to a beta...

re-add --pat_to_bowtie, because the instance in the path pointed to a beta version (2.0.0-beta7) whereas 2.1.0 is out for months
parent 5945c58a
......@@ -61,7 +61,7 @@ class Bismark (Analysis):
self.args += " --non_directional"
if bowtie2:
self.args += " --bowtie2"
self.args += " --bowtie2 --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2"))
def process(self):
......
......@@ -55,7 +55,7 @@ class BismarkGenomePreparation (Component):
self.databank_directory = self.output_directory
self.args = ""
if bowtie2:
self.args = " --bowtie2"
self.args = " --bowtie2 --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2"))
self.stderr = os.path.join(self.output_directory, 'bismark_genome_preparation.stderr')
self.stdout = os.path.join(self.output_directory, "bismark_genome_preparation.stdout")
......
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