Xce dev tk 2018 06 19 (#179)

* bug fix: dimple failed to run on csh due to DLS specific commands * bug fix: pandda.analyse fails to run on local machine in tcsh shell * declared v1.2.1 after csh related bug fixes
xchem · Jun 20, 2018 · 5f00f81 · 5f00f81
1 parent b0377d4
commit 5f00f81
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Showing 4 changed files with 26 additions and 12 deletions.
diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py
@@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object):
 
     def settings(self, xce_object):
         # set XCE version
-        xce_object.xce_version = 'v1.2'
+        xce_object.xce_version = 'v1.2.1'
 
         # general settings
         xce_object.allowed_unitcell_difference_percent = 12

diff --git a/lib/XChemLog.py b/lib/XChemLog.py
@@ -26,7 +26,7 @@ def create_logfile(self,version):
             '     #                                                                     #\n'
             '     # Version: %s                                       #\n' %pasteVersion+
             '     #                                                                     #\n'
-            '     # Date: 18/06/2018                                                    #\n'
+            '     # Date: 20/06/2018                                                    #\n'
             '     #                                                                     #\n'
             '     # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK  #\n'
             '     #          [email protected]                                 #\n'

diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py
@@ -418,13 +418,15 @@ def run(self):
             self.Logfile.insert(msg)
             return None
         else:
-            if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh':
-                source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n')
-            elif os.getenv('SHELL') == '/bin/bash' or self.use_remote:
-                source_file='export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n'
-                source_file+='source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n')
-            else:
-                source_file=''
+#            if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh':
+#                source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n')
+#            elif os.getenv('SHELL') == '/bin/bash' or self.use_remote:
+#                source_file='export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n'
+#                source_file+='source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n')
+#            else:
+#                source_file=''
+            # v1.2.1 - pandda.setup files should be obsolete now that pandda is part of ccp4
+            source_file=''
 
             if os.path.isfile(self.filter_pdb + '.pdb'):
                 print('filter pdb located')
@@ -548,6 +550,10 @@ def append_to_ignore_string(datasets_list, append_string):
             f = open('pandda.sh','w')
             f.write(Cmds)
             f.close()
+
+#            #>>> for testing
+#            self.submit_mode='local machine'
+
             if self.submit_mode=='local machine':
                 self.Logfile.insert('running PANDDA on local machine')
                 os.system('chmod +x pandda.sh')

diff --git a/lib/XChemThread.py b/lib/XChemThread.py
@@ -1159,6 +1159,14 @@ def run(self):
             else:
                 symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split('(')[0]).split()]).replace('[','').replace(']','').replace("'","").replace(',','').replace(' ','')
 
+            dls_stuff = ''
+            if os.path.isdir('/dls'):
+                dls_stuff = (
+                    'module unload ccp4\n'
+                    'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n'
+                )
+
+
             Cmds = (
                     '{0!s}\n'.format(top_line)+
                     '\n'
@@ -1168,9 +1176,9 @@ def run(self):
                     '\n'
                     'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n'
                     '\n'
-                    'module unload ccp4\n'
-                    'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n'
-                    +ccp4_scratch+
+                    + dls_stuff +
+                    '\n'
+                    + ccp4_scratch +
                     '\n'
                     '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(database,xtal,'DimpleStatus','running') +
                     '\n'