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annotate seqrequester/scripts/search.pl @ 1:1085e094cf5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
author fubar
date Sat, 13 Jul 2024 12:39:06 +0000
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1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
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1 #!/usr/bin/env perl
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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2
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3 use strict;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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4 use Time::HiRes qw(usleep nanosleep);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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5
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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6 my $order = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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7 my $weight = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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8
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9 while (scalar(@ARGV) > 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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10 my $arg = shift @ARGV;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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11
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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12 if ($arg eq "-order") {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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13 $order = shift @ARGV;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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14 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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16 if ($arg eq "-weight") {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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17 $weight = shift @ARGV;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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18 }
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19 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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20 if ($order == 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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21 die "usage: $0 -order <order>\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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22 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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23
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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24 # This scales at 4^k * 4^k -- (state vectors) * (cycle length)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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25 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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26 # time seqrequester shift -search -fast -tapmin 300000000000 -tapmax 300033333333 -order 12 -report 0.9
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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27 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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28 # The SV MUST NOT start with 0 or 1. We generate the new SR state as
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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29 #
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30 # out = rightmost 2 bits of SR
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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31 # mul = SV * out (* in GF4, operating on 2-bit tuples)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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32 # SR = (SR >> 2) ^ mul
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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33 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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34 # When the SV starts with 0, the resulting SR will always start with zero -
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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35 # it is like we simply reduce the order by one. The longest cycle in order
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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36 # 12 here is 4194304, exactly 1/4 the maximum expected, and exactly the
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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37 # length of the cycle for order 11.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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38 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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39 # When the SV starts with 1, we car simply moving the output symbol to the
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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40 # input - we turn the shift register into a cyclic shift register. The longest
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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41 # cycle in order 12 here is 'exactly' 1/3 the maximum - 5592406 out of 16777216.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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42 # I do not know why.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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43 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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44 # 3's and 2's seem interchangable; swapping all 3's and 2's in a vector
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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45 # seems to generate the same cycles length. This probably just 'reverses'
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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46 # the sequence. NOT RIGOROUSLY TESTED.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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47 #
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48 #
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49 #
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50 # valgrind --tool=callgrind --dump-instr=yes --simulate-cache=yes --collect-jumps=yes \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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51 # seqrequester shift -search -fast -tapmin 300000000000 -tapmax 300003333333 -order 12 -report 0.9
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52 # callgrind_control -h
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53 #
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54 # Hardcoded job splits.
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55 # order <= 10 - 0 digits - 1 job
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56 # order == 11 - 1 digit - 4 jobs
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57 # order == 12 - 2 digits - 16 jobs
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58 # order == 13 - 4 digits - 256 jobs
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59 # order == 14 - 6 digits - 4096 jobs
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60 # order == 15 - 8 digits - 65536 jobs
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61 # order == 16 - 11 digits - 4194304 jobs
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62 #
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63 # Times are on Ryzen 7 3700X unless noted.
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64 # Times are signifcantly worse if multiple jobs run.
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65 #
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66 # order == 12 - with prefix 5 took 1.43 minutes for 30000........ (actual) - 1024 prefixes -> 24 CPU hours
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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67 # order == 12 - with prefix 5 took 0.93 minutes for 30000........ (actual) - 1024 prefixes -> no detect version
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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68 # order == 12 - with prefix 4 took 5.75 minutes for 3000......... (actual) - 256 prefixes -> 24 CPU hours
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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69 # order == 12 - with prefix 4 took 14.03 minutes for 3000......... (actual) - 256 prefixes -> 60 CPU hours (on d)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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70 # order == 12 - with prefix 4 took 14.03 minutes for 3000......... (actual) - 256 prefixes -> but 90 minutes/job is all 24 cores are used!
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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71 # order == 12 - with prefix 3 took minutes for 300.......... (estimated) - 64 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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72 # order == 12 - with prefix 2 took minutes for 30........... (estimated) - 16 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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73 #
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74 # order == 13 - with prefix 6 took 9 minutes for 300000....... (actual) - 4096 prefixes -> 614 CPU hours
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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75 # order == 13 - with prefix 5 took 36 minutes for 30000........ (estimated) - 1024 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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76 # order == 13 - with prefix 4 took 144 minutes for 3000......... (estimated) - 256 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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77 #
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78 # order == 14 - with prefix 9 took 8 minutes for 300000000..... (actual) - 262144 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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79 # order == 14 - with prefix 8 took 32 minutes for 30000000...... (actual) - 65536 prefixes -> 35,000 CPU hours
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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80 # order == 14 - with prefix 7 took 128 minutes for 3000000....... (estimated) - 16384 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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81 #
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82 # order == 15 - with prefix 12 took 2.96 minutes for 300000000000... (actual) - 16777216 prefixes -> 827,675 CPU hours
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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83 # order == 15 - with prefix 12 took 0.28 minutes for 300000000000... (actual) - 16777216 prefixes -> no detect version
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
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84 # order == 15 - with prefix 11 took 9.13 minutes for 30000000000.... (actual) - 4194304 prefixes -> 638,233 CPU hours
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
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85 # order == 15 - with prefix 10 took 39.38 minutes for 3000000000..... (actual) - 1048576 prefixes -> 688,273 CPU hours (78.6 years)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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86 # order == 15 - with prefix 10 took 3.76 minutes for 3000000000..... (actual) - 1048576 prefixes -> no detect version --
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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87 # order == 15 - with prefix 10 took 4.11 minutes for 3000000000..... (actual) - 1048576 prefixes -> no detect version -- with 16 copies running
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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88 # order == 15 - with prefix 9 took minutes for 300000000...... (estimated) - 262144 prefixes ->
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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89 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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90 # CL time
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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91 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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92 # BD time
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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93 # time seqrequester shift -search -fast -order 21 -report 0.0 -tapmin 300000000000000000000 -tapmax 300000000000000003333 -weight 3
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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94 # 66069.844u 0.283s 18:21:14.56 99.9% 177+817k 0+0io 7pf+0w
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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95 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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96 # order = 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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97 my @plen = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 9, 11, 13, 15, 17, 19, 0 );
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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98
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99 # prefix 5 for 15 is way too big. this resulted in 256 jobs (1024 prefixes,
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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100 # but only the ones starting with 3 are computed). each job is taking a bit
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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101 # more than 100 hours.
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102 # wallclock 415000s (115 hours x 256 jobs = 29440 cpu hours)
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103 # user 381110s (remarkably constant)
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104 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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105 # job scaling should be x4 for each search, and there are x4 more vectors to try.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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106 # so for constant job time, we need to increase the prefix length by 2 for each.
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107
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108 # prefix 9 for 16 resulted in the last job 12550u 3:30 on bv (x 65536 jobs = 229376 cpu hours).
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109
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110
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111 print STDERR "Building job names with $plen[$order] components.\n";
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112
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113 my @alljobs = ( "0", "1", "2", "3" );
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114 my @subjobs;
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115
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116 for (my $p=1; $p < $plen[$order]; $p++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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117 my @tmpjobs = @alljobs;
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118 undef @alljobs;
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119
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120 foreach my $e (@tmpjobs) {
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121 push @alljobs, "0$e";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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122 push @alljobs, "1$e";
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123 push @alljobs, "2$e";
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124 push @alljobs, "3$e";
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125 }
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126 }
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127
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128 print STDERR "Filtering job names.\n";
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129
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130 foreach my $pp (@alljobs) {
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131 push @subjobs, $pp if (($pp =~ m/^0/) && ($order < 14)); # Ignore 0, no complete cycles in here.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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132 push @subjobs, $pp if (($pp =~ m/^1/) && ($order < 14)); # Ignore 1, no complete cycles in here.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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133 push @subjobs, $pp if (($pp =~ m/^2/) && ($order < 14)); # Ignore 2, seems to be just a dual of 3.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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134 push @subjobs, $pp if (($pp =~ m/^3/) && ($order < 22)); # Always use 3.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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135 }
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136
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137 @subjobs = sort { $b cmp $a } @subjobs;
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138
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139 my $tJobs = scalar(@alljobs);
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140 my $sJobs = scalar(@subjobs);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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141
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142 print STDERR "Created $tJobs jobs.\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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143 print STDERR "Submitting $sJobs jobs.\n";
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144
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145
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146 my $bgn = "0" x ($order - $plen[$order]);
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147 my $end = "3" x ($order - $plen[$order]);
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148
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149 open(F, "> o${order}w${weight}.dat");
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150
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151 foreach my $pp (@subjobs) {
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152 print F "$pp\n";
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153 }
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154
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155 close(F);
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156
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157
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158
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159 open(F, "> o${order}w${weight}.sh");
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160 print F "#!/bin/sh\n";
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161 print F "\n";
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162 print F "\n";
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163 print F "if [ x\$SGE_TASK_ID = x -o x\$SGE_TASK_ID = xundefined -o x\$SGE_TASK_ID = x0 ]; then\n";
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164 print F " j=\$1\n";
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165 print F "else\n";
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166 print F " j=\$SGE_TASK_ID\n";
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167 print F "fi\n";
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168 print F "if [ x\$j = x ]; then\n";
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169 print F " echo Error: I need SGE_TASK_ID set, or a job index on the command line.\n";
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170 print F " exit\n";
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171 print F "fi\n";
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172 print F "\n";
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173 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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174 print F "p=`head -n \$j o${order}w${weight}.dat | tail -n 1`";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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175 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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176 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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177 print F "if [ -e \"o${order}w${weight}-out/o${order}w${weight}p\$p.out\" ]; then\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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178 print F " echo \"o${order}w${weight}p\$p.out exists, it's done!\"\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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179 print F " exit 0\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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180 print F "fi\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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181 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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182 print F "if [ ! -d \"o${order}w${weight}-out\" ]; then\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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183 print F " mkdir -p o${order}w${weight}-out\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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184 print F "fi\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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185 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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186 print F "/work/seqrequester/FreeBSD-amd64/bin/seqrequester \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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187 print F " shift -search -fast \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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188 print F " -order $order \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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189 print F " -weight $weight \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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190 print F " -report 0.0 \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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191 print F " -tapmin \${p}$bgn \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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192 print F " -tapmax \${p}$end \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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193 print F "> o${order}w${weight}-out/o${order}w${weight}p\$p.out.WORKING \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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194 print F "&& \\\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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195 print F "mv o${order}w${weight}-out/o${order}w${weight}p\$p.out.WORKING o${order}w${weight}-out/o${order}w${weight}p\$p.out\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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196 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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197 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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198 print F "#\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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199 print F "# qsub -h -cwd -j y -o o${order}w${weight}-err/o${order}w${weight}-\\\$TASK_ID.err -l memory=1g -t 1-$sJobs -N o${order}w${weight} ./o${order}w${weight}.sh\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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200 print F "#\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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201 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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202 print F "exit 0\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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203 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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204
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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205 close(F);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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206
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207 chmod(0755, "o${order}w${weight}.sh");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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208
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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209 system("mkdir o${order}w${weight}-err");
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210 system("mkdir o${order}w${weight}-out");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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211
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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212 print "qsub -h -cwd -j y -o o${order}w${weight}-err/o${order}w${weight}-\\\$TASK_ID.err -l memory=1g -t 1-$sJobs -N o${order}w${weight} ./o${order}w${weight}.sh\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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213 system("qsub -h -cwd -j y -o o${order}w${weight}-err/o${order}w${weight}-\\\$TASK_ID.err -l memory=1g -t 1-$sJobs -N o${order}w${weight} ./o${order}w${weight}.sh") if (1);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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214
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215 exit;