check diamond

panX.py

@@ -163,6 +163,8 @@
 #species=params.species_name
 
 programs={'mcl':'mcl', 'mafft':'mafft', 'fasttree':'FastTree', 'raxml':'raxmlHPC'}
+if params.diamond_path=='':
+ programs['diamond']='diamond'
 for program_alias, program_name in programs.items():
  passed=False
  ## check whether program_alias exists (if yes, test passed)
@@ -173,7 +175,13 @@
  continue
  ## if the program is not installed, exit
  if not passed:
- print 'program '+program_name+' not found, please install it.'
+ if program_name=='diamond':
+ warning='\ndiamond not found:\nplease make sure that diamond is installed '+\
+ 'and diamond binary file is included in the executable search path (e.g.: /usr/bin/diamond);\n'+\
+ 'alternatively, one can specify diamond path via the parameter -dmp (e.g.: ./panX.py -dmp /mypath/diamond -fn ...)'
+ print warning
+ else:
+ print 'program '+program_name+' not found, please install it.'
  exit()
 
 myPangenome=pangenome(