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root/gclib/scripts/pexo_run.csh.psx
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 1042 byte(s)
Log Message:
Line File contents
1 #!/bin/tcsh -f
2 #
3 # 1 2 3 4 5 6 7
4 #my ($file, $numpass, $slice_num, $last, $skipped, $total, $user)=@ARGV;
5 set fq=$1
6 set numpass=$2
7 set slnum=$3
8 set islast=$4
9 set slskipped=$5
10 set sltotal=$6
11 set fesi=$7
12
13 set esf=$fesi:t
14 set espath=$fesi:h
15 set fb=$esf:r
16 set fb=$fb:r
17 set srvlog=srv_${fb}_$slnum.log
18 set exout=$fq.exout
19
20 #goto TEST_LOOP
21
22 set sv=`ps auxwww | grep exonerate-server | grep 'port 3804'`
23
24 if ( $#sv > 2 ) then
25 echo "Existing server on this machine on port 3804, aborting.."
26 exit 241
27 endif
28
29 # echo "Launching server.."
30 set cpath = `pwd`
31 cd $espath
32 exonerate-server --maxconnections 1 --verbosity 1 --proteinwordlen 4 --port 3804 $esf >& $cpath/$srvlog &
33 set bpid = $!
34 #echo "Background process ID= $bpid"
35
36 cd $cpath
37
38 while ( `grep listening $srvlog`"x" == "x" )
39 sleep 2
40 end
41 sleep 2
42 echo "Running: pexo_slice.pl -o $exout $fq"
43 pexo_slice.pl -o $exout $fq
44 /bin/rm -f $fq
45 fltexonerate -p 75 -c 70 < $exout > $exout.p75c70.gff3
46 echo '<Done.' >> /dev/stderr
47 sleep 2
48
49 kill $bpid
50
51 exit 0

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