fixed error with shlex

proost · Nov 28, 2016 · f95cd37 · f95cd37
1 parent a37b7d0
commit f95cd37
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/pipeline/base.py b/pipeline/base.py
@@ -43,15 +43,15 @@ def __init__(self, config, data, enable_log=False):
         self.mcl_cmd = self.cp['TOOLS']['mcl_cmd']
         self.mcxdeblast_cmd = self.cp['TOOLS']['mcxdeblast_cmd']
 
-        self.qsub_bowtie = shlex.split(self.cp['TOOLS']['qsub_bowtie'])
-        self.qsub_trimmomatic = shlex.split(self.cp['TOOLS']['qsub_trimmomatic'])
-        self.qsub_tophat = shlex.split(self.cp['TOOLS']['qsub_tophat'])
-        self.qsub_htseq_count = shlex.split(self.cp['TOOLS']['qsub_htseq_count'])
-        self.qsub_interproscan = shlex.split(self.cp['TOOLS']['qsub_interproscan'])
-        self.qsub_pcc = shlex.split(self.cp['TOOLS']['qsub_pcc'])
-        self.qsub_mcl = shlex.split(self.cp['TOOLS']['qsub_mcl'])
-        self.qsub_orthofinder = shlex.split(self.cp['TOOLS']['qsub_orthofinder'])
-        self.qsub_mcxdeblast = shlex.split(self.cp['TOOLS']['qsub_mcxdeblast'])
+        self.qsub_bowtie = shlex.split(self.cp['TOOLS']['qsub_bowtie'].strip('\''))
+        self.qsub_trimmomatic = shlex.split(self.cp['TOOLS']['qsub_trimmomatic'].strip('\''))
+        self.qsub_tophat = shlex.split(self.cp['TOOLS']['qsub_tophat'].strip('\''))
+        self.qsub_htseq_count = shlex.split(self.cp['TOOLS']['qsub_htseq_count'].strip('\''))
+        self.qsub_interproscan = shlex.split(self.cp['TOOLS']['qsub_interproscan'].strip('\''))
+        self.qsub_pcc = shlex.split(self.cp['TOOLS']['qsub_pcc'].strip('\''))
+        self.qsub_mcl = shlex.split(self.cp['TOOLS']['qsub_mcl'].strip('\''))
+        self.qsub_orthofinder = shlex.split(self.cp['TOOLS']['qsub_orthofinder'].strip('\''))
+        self.qsub_mcxdeblast = shlex.split(self.cp['TOOLS']['qsub_mcxdeblast'].strip('\''))
 
         self.genomes = self.dp['GLOBAL']['genomes'].split(';')
         self.email = None if self.dp['GLOBAL']['email'] == 'None' else self.cp['DEFAULT']['email']

diff --git a/pipeline/transcriptome.py b/pipeline/transcriptome.py
@@ -29,7 +29,7 @@ def prepare_genome(self):
             os.makedirs(os.path.dirname(output), exist_ok=True)
             shutil.copy(con_file, output + '.fa')
 
-            command = ["qsub"] + self.qsub_bowtie + ["in=" + con_file + ",out=" + output, filename]
+            command = ["qsub"] + self.qsub_bowtie + ["-v", "in=" + con_file + ",out=" + output, filename]
 
             subprocess.call(command)