Cloning group loop

([iter],[grp]) ; Cloning group loop
;
; SOURCE: spider/docs/techs/recon/newprogs/pub_ref_loop_clone.pam
;         New                                    ArDean Leith Jan 2009
;         New variable definitions               ArDean Leith Mar 2010
;         recursive bug                          ArDean Leith May 2010
;         null copy on [iter_vft]                ArDean Leith Aug 2010
;         New variable definitions               ArDean Leith Jan 2011
;         Dala removal, doc files not cloned     ArDean Leith Jan 2012
;
; PURPOSE: Runs on compute nodes to copy 'grploop files' to local disk
;
; CALLED FROM: pub_refine_start 
;
; Files are set in: refine settings refine settings.pam
; 
; INPUT REGISTERS:
;    [iter]               Iteration counter      (Varies with iter)
;    [grp]                Defocus group          (Varies with group)
;
; '##' denotes iteration,  '##+' denotes next iteration, and '***' denotes group
; INPUT FILES:  (Copied from master node or created/used on compute node)
;    [sel_group]          input/sel_group         Group selection doc file
;    [sel_particles]      input/select_***        Particle selection file          
;    [unaligned_images]   input/data***           Unaligned stacked image files      
;    [iter_refangs]       work/ref_angs_##        Ref. angles doc file                  
;    [temp_ctf_file]      work/ctf***             CTF corrected volume from prepare  
;    [iter_vft]           final/vft##             Current filtered volume     (Optional)
;    [grp_resol]                                  Group resolution file       (Optional)
; ---------------------------------------------------------------------

; Clear temp directory and create temp local dir., divert errors to junk
 VM
   \rm -rf [temp_local_dir]/input [temp_local_dir]/final [temp_local_dir]/work >& /dev/null

 ; Create temp local dir., Divert errors to junk
 VM
   mkdir -p [temp_local_dir] [temp_local_dir]/input [temp_local_dir]/final [temp_local_dir]/work >& /dev/null

 VM                                 ; So anyone can delete it
   chmod 777 [temp_local_dir]/input [temp_local_dir]/final [temp_local_dir]/work >& /dev/null

 VM                                 ; Not used for small angle refinement
   \cp [iter_vft].$DATEXT             [temp_local_dir][iter_vft].$DATEXT >& /dev/null
 VM
   \cp [iter_refangs].$DATEXT         [temp_local_dir][iter_refangs].$DATEXT 
 VM
   \cp [temp_ctf_file].$DATEXT        [temp_local_dir][temp_ctf_file].$DATEXT 
 VM
   \cp [sel_particles].$DATEXT        [temp_local_dir][sel_particles].$DATEXT 
 VM
   \cp [group_align].$DATEXT          [temp_local_dir][group_align].$DATEXT 
 VM
   \cp [unaligned_images].$DATEXT     [temp_local_dir][unaligned_images].$DATEXT 

 ;;VM ; NECESSARY??
 ;;  \cp [grp_resol].$DATEXT            [temp_local_dir][grp_resol].$DATEXT >& /dev/null

 ; Save current output file locations for declone (Saves current value of variable)

 GLO [master_next_group_vol]    = [next_group_vol] 
 GLO [master_next_group_fsc]    = [next_group_fsc] 

 ; Redefine current file locations for input files

 GLO [iter_vft]                = '[temp_local_dir]/'[iter_vft] 
 GLO [iter_refangs]            = '[temp_local_dir]/'[iter_refangs] 
 GLO [temp_ctf_file]           = '[temp_local_dir]/'[temp_ctf_file] 
 GLO [sel_particles]           = '[temp_local_dir]/'[sel_particles] 
 GLO [group_align]             = '[temp_local_dir]/'[group_align] 
 GLO [unaligned_images]        = '[temp_local_dir]/'[unaligned_images] 
          
 ; Redefine current file locations for output files from compute node

 GLO [next_group_vol]          = '[temp_local_dir]/'[next_group_vol] 
 GLO [next_group_fsc]          = '[temp_local_dir]/'[next_group_fsc] 

 RE
;