#! /bin/bash -l
####/bin/sh
# aadrosblast.sh
# blast a bunch of genomes
# sample script for bioinformatics data-grid methods (parallelize by data splitting)
# using ibm LoadLeveler

SHARED=$HOME/scratch
ACCOUNT=TG-xxx
blbin=$HOME/bio/blast/bin
jalib=$HOME/bio/blast/lib/java
ncbibin=$HOME/bio/ncbi/bin
# or ncbibin=/N/soft/linux-sles9-ppc64/ncbi-2.2.16/bin/
# mpiblast=$HOME/bio/iuparblast/ncbi/bin

# gilbertd@BigRed:~/bio/blast/drostand> ls dsec*aa.gz
# dsec_bren_nsc.aa.gz       dsec_caf1_NCBI_GNO.aa.gz  dsec_glean1.aa.gz
# dsec_caf1_DGIL_SNO.aa.gz  dsec_genewise1.aa.gz      dsec_gleanr.aa.gz
## about 16k to 30k prots/predictor : split about 10x each, vs all together in target db

qsplist="dsec_caf1_NCBI_GNO dsec_genewise1 dsec_gleanr dsec_bren_nsc dsec_caf1_DGIL_SNO dsec_glean1"

protdir="$SHARED/prots/aadros/"
outdir="$SHARED/prots/aadros/"

targetnm="dsecdb"
targetdb="$SHARED/prots/aadros/dsec_all.aa"

# gunzip -c dsec*.aa.gz > $targetdb
# $ncbibin/formatdb -p T -i $targetdb
# == 51 MB .psq database
# job size: one part 2000q x target 150,000 =~ 15 min?

npart=5

for qspp in $qsplist
{
 qfasta="${qspp}.aa"
 $blbin/dgfasplit.pl -JA $jalib -n $npart -in $protdir/$qfasta
 
 for qpart in $protdir/$qfasta-*
 {
   [ -f $qpart ] || continue; 
   qp=`echo  $qpart| sed -e's/.*a-//;'`

   ## [ $qp == "01" ] && continue; 
   ## [ $qp != "01" ] && continue; 

   jobn=run-${qspp}-${targetnm}.$qp 
   outn=$outdir/${qspp}-${targetnm}.$qp
   cat > $jobn <<EOJ
#! /bin/bash -l
## IBM LoadLeveler job, llsubmit
# @ class = MED
# @ account_no = $ACCOUNT
# @ wall_clock_limit = 01:00:00
# @ error   = $outn.err
# @ output  = $outn.out
# @ notification = always
# @ environment=COPY_ALL;
# @ queue

$ncbibin/blastall \\
  -p blastp -a 2 -m 9 -e 0.00001 \\
  -o $outn.blastp \\
  -d $targetdb \\
  -i $qpart

EOJ
  llsubmit $jobn


#  break
## test 1 first
  }
}

# -g F -a 1 -b 10 -v 10 

## other LL metacomments
# @ wall_clock_limit = 02:00:00
# @ class = FAST  : 15 minutes, max slots=15
# @ class = MED
# @ job_type = parallel
# @ node = 4
# @ tasks_per_node = 2

# gilbertd@BigRed:~/bio/blast/drostand> llclass
# Name                 MaxJobCPU     MaxProcCPU  Free   Max Description          
#                     d+hh:mm:ss     d+hh:mm:ss Slots Slots                      
# --------------- -------------- -------------- ----- ----- ---------------------
# FAST                  04:00:00       00:15:00    15    16 Fast Queue for Debuging
# PU_LOW            448+00:00:00     7+00:00:00   252   252 Low queue for Purdue for up to 16 nodes
# PU_MED           1792+00:00:00     7+00:00:00   252   252 Med queue for Purdue for up to 64 nodes
# BIG              2048+00:00:00     2+00:00:00   191  1544 Big Queue for up to 256 nodes
# PU_HIGH          3584+00:00:00     7+00:00:00   512   512 High queue for Purdue for up to 128 nodes
# MED              3584+00:00:00    14+00:00:00    87  1432 Intermediate Queue for up to 64 nodes
# PU_WIDE          7168+00:00:00     7+00:00:00  1016  1016 Wide queue for Purdue for up to 256 nodes
# --------------------------------------------------------------------------------
# "Maximum Slots" value of the class "FAST" is constrained by the MAX_STARTERS limit(s).
# "Free Slots" values of the classes "FAST", "BIG", "MED" are constrained by the MAX_STARTERS limit(s).

# llclass -l
# =============== Class FAST ===============
#        Class_comment: Fast Queue for Debuging
#     Wall_clock_limit: 00:15:00, undefined (900 seconds, undefined)
# Def_wall_clock_limit: 00:15:00, undefined (900 seconds, undefined)
#        Job_cpu_limit: 04:00:00, undefined (14400 seconds, undefined)
#            Cpu_limit: 00:15:00, undefined (900 seconds, undefined)
#        Maximum_slots: 16
# =============== Class MED ===============
#        Class_comment: Intermediate Queue for up to 64 nodes
#     Wall_clock_limit: 14+00:00:00, undefined (1209600 seconds, undefined)
# Def_wall_clock_limit: 02:00:00, undefined (7200 seconds, undefined)
#        Job_cpu_limit: 3584+00:00:00, undefined (309657600 seconds, undefined)
#            Cpu_limit: 14+00:00:00, undefined (1209600 seconds, undefined)
#        Maximum_slots: 1432