([iter],[grp])
; Cloning endmerge
;
; SOURCE: spider/docs/techs/recon/newprogs/pub_ref_clone.pam
; New ArDean Leith Jan 2009
; New variable definitions ArDean Leith Jun 2010
; New variable definitions ArDean Leith Jan 2011
; Dala removal ArDean Leith Jan 2012
;
; PURPOSE: Runs on compute nodes to copy 'endmerge files' from master disk to local disk
;
; CALLED FROM: pub_refine_start
;
; INPUT REGISTERS:
; [iter] Alignment step 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] work/select_*** Particle selection doc file
; [next_group_align] final/align_##+_*** Alignment parameter doc file
;
; ---------------------------------------------------------------------
[next-iter] = [iter] + 1
; Clear temp directory and create temp local dir., divert errors to junk
VM
\rm -rf [temp_local_dir]/input [temp_local_dir]/work [temp_local_dir]/final >& /dev/null
; Create temp local dir. Divert errors to junk
VM
mkdir -p [temp_local_dir] [temp_local_dir]/input [temp_local_dir]/work [temp_local_dir]/final >& /dev/null
VM ; So anyone can delete it
chmod 777 [temp_local_dir]/input [temp_local_dir]/work [temp_local_dir]/final >& /dev/null
; Copy files from master disk to local disk
VM
\cp [sel_group].$DATEXT [temp_local_dir][sel_group].$DATEXT
VM
\cp [sel_particles].$DATEXT [temp_local_dir][sel_particles].$DATEXT
VM
\cp [next_group_align].$DATEXT [temp_local_dir][next_group_align].$DATEXT
; Save current output file locations for declone ------------
GLO [master_next_group_bpr] = [next_group_bpr]
GLO [master_next_group_ofsc] = [next_group_ofsc]
; Redefine current file locations for input files -----------
GLO [sel_group] = '[temp_local_dir]'[sel_group]
GLO [sel_particles] = '[temp_local_dir]'[sel_particles]
GLO [next_group_align] = '[temp_local_dir]'[next_group_align]
; Redefine current file locations for output files ---------
GLO [next_group_bpr] = '[temp_local_dir]'[next_group_bpr]
GLO [next_group_ofsc] = '[temp_local_dir]'[next_group_ofsc]
RE
;