feat: add structure_analysis_enabled option within conbox commands

aria/conbox/conf/config.ini

@@ -201,6 +201,7 @@ water_refinement_solvent:                   water
 water_refinement_n_structures:              10
 water_refinement_enabled:                   no
 water_refinement_write_solvent_molecules:   no
+structure_analysis_enabled:                 yes
 procheck_executable:
 procheck_enabled:                           yes
 prosa_executable:

aria/conbox/templates/aria_project_v2.3.7.xml

@@ -72,7 +72,7 @@
     <water_refinement solvent="${water_refinement_solvent}" n_structures="${water_refinement_n_structures}" enabled="${water_refinement_enabled}" write_solvent_molecules="${water_refinement_write_solvent_molecules}"/>
   </protocol>
   <analysis>
-    <structures_analysis enabled="yes"/>
+    <structures_analysis enabled="${structure_analysis_enabled}"/>
     <procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
     <prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
     <whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>

aria/core/cns.py

@@ -1991,7 +1991,7 @@ class CNS(StructureEngine):
         cns_input = os.path.join(infra.get_cns_protocols_path(),
                                  '%s.inp' % cns_script)
 
-        # name of local output file
+        # name of local output filesge_job_shell
         cns_output = '%s.out' % os.path.basename(cns_script)
 
         if use_default_executable or self.use_condor:
@@ -2027,7 +2027,7 @@ class CNS(StructureEngine):
             # job_name for queue (not mandatory but usefull)
             sge_job_name = os.path.basename(cns_working_dir)
             d['sge_job_name'] = sge_job_name
-            d['sge_job_shell'] = '/bin/csh'
+            d['sge_job_shell'] = '/bin/csh -f'
             # d['sge_job_hostname'] = '%(sge_job_hostname)s'
 
             script = CSH_SCRIPT_REFINE % d