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Mark Howison committed cca386a

sampler: fixed calls to RSEM (1.2.15)

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  • Parent commits 8240d7f
  • Branches issue-7

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Files changed (1)

File gabi/sampler.py

                 insert_max = '%.0f' % (self.insert_mean + 2*self.insert_stdev)
                 try:
                     subprocess.check_call(
-                        [ "rsem-prepare-reference", filename, self.rsempath ],
+                        [ "rsem-prepare-reference", "--bowtie", filename, self.rsempath ],
                         stdout=f, stderr=f)
                     subprocess.check_call(
                         [
-                            "rsem-calculate-expression", "--paired-end",
+                            "rsem-calculate-expression",
+                            "--num-threads", self.threads, "--paired-end",
                             "--fragment-length-min", insert_min,
                             "--fragment-length-max", insert_max,
-                            "-1", self.reads[0], "-2", self.reads[1],
-                            "-p", self.threads, self.rsempath
+                            self.reads[0], self.reads[1],
+                            self.rsempath, self.rsempath
                         ],
                         stdout=f, stderr=f)
                     subprocess.check_call(