Commit d7621880 authored by Jerome Mariette's avatar Jerome Mariette
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parent dca61db6
......@@ -400,7 +400,7 @@ class RunAssembly (Analysis):
self._create_and_archive(result_files, self.archive_name)
def get_version(self):
cmd = [self.get_exec_path("RunAssembly"), "--version"]
cmd = [self.get_exec_path("runAssembly"), "--version"]
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
stdout, stderr = p.communicate()
return stdout.split()[1]
......@@ -419,7 +419,7 @@ class RunAssembly (Analysis):
o_large_contig_fasta_files = self.get_outputs('{basename_woext}/454LargeContigs.fna', self.input_files)
o_large_contig_qual_files = self.get_outputs('{basename_woext}/454LargeContigs.qual', self.input_files)
# define command line
run_assembly = ShellFunction(self.get_exec_path("RunAssembly") + " " + self.options + " -o $2 $1 > $3",
run_assembly = ShellFunction(self.get_exec_path("runAssembly") + " " + self.options + " -o $2 $1 > $3",
cmd_format='{EXE} {IN} {OUT}')
run_assembly = MultiMap(run_assembly, self.input_files, [self.output_dirs, self.stdouts,
o_ace_files, o_metrics_files, o_large_contig_fasta_files,
......
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