modif to make methylseq work on genobioinfo

workflows/methylseq/components/bismark.py

@@ -99,8 +99,8 @@ class Bismark (Analysis):
                 # 2 bowtie process are launch in directional mode so divided allocated cpu for each bowtie
                 self.args += " --p "+ str(int(self.nb_proc/2))
             self.args += " --bowtie2"
-            if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
-                self.args += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
+            #if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
+            #    self.args += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
              
         
         self.options = self.args + " | Databank " + os.path.basename(self.reference_genome)

workflows/methylseq/components/bismark_genome_preparation.py

@@ -57,8 +57,8 @@ class BismarkGenomePreparation (Component):
         
         if not self.bowtie1 : 
             btw_param = " --bowtie2"
-            if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
-                btw_param += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
+            #if not os.path.dirname(self.get_exec_path("bowtie2")) == "" :
+            #    btw_param += " --path_to_bowtie " + os.path.dirname(self.get_exec_path("bowtie2")) 
             self.args += "\\'"+btw_param+"\\'"
             
         

workflows/methylseq/components/trim_galore.py

@@ -80,12 +80,12 @@ class TrimGalore (Analysis):
     def process(self):
         
         if self.is_paired: 
-            self.add_shell_execution( self.get_exec_path("trim_galore") + " " + self.options + \
+            self.add_shell_execution( "module load bioinfo/Cutadapt/1.8.3;module load bioinfo/TrimGalore/0.4.5;"+ self.get_exec_path("trim_galore") + " " + self.options + \
                             " -o " + self.output_directory + " $1 $2 >$3 2>> $4 ", 
                             cmd_format='{EXE} {IN} {OUT}', map=True, inputs=[self.input_files_R1, self.input_files_R2], 
                             outputs=[self.stderrs,self.stdouts,self.output_files_R1,self.output_files_R2,self.report_files_R1,self.report_files_R2])
         else : 
-            self.add_shell_execution( self.get_exec_path("trim_galore") + " " + self.options + \
+            self.add_shell_execution( "module load bioinfo/Cutadapt/1.8.3;module load bioinfo/TrimGalore/0.4.5;"+ self.get_exec_path("trim_galore") + " " + self.options + \
                             " -o " + self.output_directory + " $1 > $2 2>> $3 ", cmd_format='{EXE} {IN} {OUT}', map=True,
                             inputs=[self.input_files_R1], outputs=[self.stderrs,self.stdouts,self.output_files_R1,self.report_files_R1])