1#!/usr/local/bin/perl -w 2use strict; 3use Cwd qw(cwd); 4my ($O, $cmd); 5my $ACC = 'ERR2950949'; 6 7my $ALL = 1; 8 9my $DEBUG = ''; 10#$DEBUG = '-+ VFS'; 11 12my $PRF_DEBUG = ''; # '-vv'; 13 14my $VERBOSE = 0; 15#$VERBOSE = 1; # print what's executed' 16#$VERBOSE = 2; # print commands 17#$VERBOSE = 3; # print command output 18 19`echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > k`; 20 21`rm -r ERR2950949`; 22 23if ($ALL) { 24########## use site repository (if exists) from default configuration ########## 25print "########################################################\n" if($VERBOSE); 26print "vdb-dump - use site repository\n" if ($VERBOSE); 27$cmd = "vdb-dump $ACC -R 1489067 $DEBUG -CREAD"; 28print "$cmd\n" if ($VERBOSE > 1); 29$O = `$cmd 2>&1`; 30print $O if ($VERBOSE > 2); 31die if ($?); 32} 33 34if ($ALL) { 35print "########################################################\n" if($VERBOSE); 36print "fastq-dump - use site repository\n" if ($VERBOSE); 37$cmd = "fastq-dump $ACC -N 1489067 -X 1489067 $DEBUG -Z"; 38print "$cmd\n" if ($VERBOSE > 1); 39$O = `$cmd 2>&1`; 40print $O if ($VERBOSE > 2); 41die if ($?); 42} 43 44########## use remote repository ########## 45`echo '/repository/site/disabled = "true"' >> k`; 46 47if ($ALL) { 48print "########################################################\n" if($VERBOSE); 49print "vdb-dump - use remote repository\n" if ($VERBOSE); 50$cmd = "vdb-dump $ACC -R 1489067 $DEBUG -CREAD"; 51print "$cmd\n" if ($VERBOSE > 1); 52$O = `$cmd 2>&1`; 53print $O if ($VERBOSE > 2); 54die if ($?); 55} 56 57if ($ALL) { 58print "########################################################\n" if($VERBOSE); 59print "fastq-dump - use remote repository\n" if ($VERBOSE); 60$cmd = "fastq-dump $ACC -N 1489067 -X 1489067 $DEBUG -Z"; 61print "$cmd\n" if ($VERBOSE > 1); 62$O = `$cmd 2>&1`; 63print $O if ($VERBOSE > 2); 64die if ($?); 65} 66 67 68########## prefetch to AD ########## 69if ($ALL) { 70print "########################################################\n" if($VERBOSE); 71print "prefetch to AD\n" if ($VERBOSE); 72$cmd = "prefetch $ACC $DEBUG $PRF_DEBUG"; 73print "$cmd\n" if ($VERBOSE > 1); 74$O = `$cmd 2>&1`; 75print $O if ($VERBOSE > 2); 76die if ($?); 77 78`echo '/repository/remote/disabled = "true"' >> k`; 79} 80 81 82if ($ALL) { 83print "########################################################\n" if($VERBOSE); 84print "vdb-dump - use AD\n" if ($VERBOSE); 85$cmd = "vdb-dump $ACC -R 1489067 $DEBUG -CREAD"; 86print "$cmd\n" if ($VERBOSE > 1); 87$O = `$cmd 2>&1`; 88print $O if ($VERBOSE > 2); 89die if ($?); 90} 91 92if ($ALL) { 93print "########################################################\n" if($VERBOSE); 94print "fastq-dump - use AD repository\n" if ($VERBOSE); 95$cmd = "fastq-dump $ACC -N 1489067 -X 1489067 $DEBUG -Z"; 96print "$cmd\n" if ($VERBOSE > 1); 97$O = `$cmd 2>&1`; 98print $O if ($VERBOSE > 2); 99die if ($?); 100} 101 102$O = `rm -rv $ACC`; die if ($?); 103print $O if ($VERBOSE > 2); 104 105########## prefetch to user repository ########## 106my $cwd = cwd(); 107`echo '/LIBS/GUID = "8test002-6ab7-41b2-bfd0-prefetchpref"' > k`; 108`echo '/repository/site/disabled = "true"' >> k`; 109`echo '/repository/user/main/public/apps/refseq/volumes/refseq = "refseq"'>> k`; 110`echo '/repository/user/main/public/apps/sra/volumes/sraFlat = "sra" '>> k`; 111`echo '/repository/user/main/public/apps/wgs/volumes/wgsFlat = "wgs"' >> k`; 112`echo '/repository/user/main/public/root = "$cwd"\n' >> k`; 113 114if ($ALL) { 115print "########################################################\n" if($VERBOSE); 116print "prefetch to user repository\n" if ($VERBOSE); 117$cmd = "prefetch $ACC $DEBUG $PRF_DEBUG"; 118print "$cmd\n" if ($VERBOSE > 1); 119$O = `$cmd 2>&1`; 120print $O if ($VERBOSE > 2); 121die if ($?); 122 123`echo '/repository/remote/disabled = "true"' >> k`; 124} 125 126if ($ALL) { 127print "########################################################\n" if($VERBOSE); 128$_ = `which srapath`; chomp; 129$_ = readlink ( $_ ); 130$_ = `which $_`; chomp; 131$_ = readlink($_); 132$_ = `which $_`; chomp; 133if (-l $_) { 134 print "skipped(remote dsb): vdb-dump - use user repository\n" if ($VERBOSE); 135} else { 136 print "vdb-dump - use user repository\n" if ($VERBOSE); 137 $cmd = "vdb-dump $ACC -R 1489067 $DEBUG -CREAD"; 138 print "$cmd\n" if ($VERBOSE > 1); 139 $O = `$cmd 2>&1`; 140 print $O if ($VERBOSE > 2); 141 die if ($?); 142} 143} 144 145if ($ALL) { 146print "########################################################\n" if($VERBOSE); 147$_ = `which srapath`; chomp; 148$_ = readlink ( $_ ); 149$_ = `which $_`; chomp; 150$_ = readlink($_); 151$_ = `which $_`; chomp; 152if (-l $_) { 153 print "skipped(remote dsb): fastq-dump - use user repository\n" if ($VERBOSE); 154} else { 155 print "fastq-dump - use user repository\n" if ($VERBOSE); 156 $cmd = "fastq-dump $ACC -N 1489067 -X 1489067 $DEBUG -Z"; 157 print "$cmd\n" if ($VERBOSE > 1); 158 $O = `$cmd 2>&1`; 159 print $O if ($VERBOSE > 2); 160 die if ($?); 161} 162} 163