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1 #!/usr/bin/perl
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2
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3 ## NB: THIS TOOL ASSUMES EMAIL ADDRESSES ARE GALAXY LOGINS
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4 ## MODIFICATIONS WILL BE REQUIRED IF YOU USE LDAP AUTHENTICATION
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5
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6 use warnings;
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7 use strict;
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8 use Cwd qw/abs_path/;
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9 use Env qw/EMAIL/;
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10 use Getopt::Long;
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11
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12 ## SETTINGS
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13 my $queue_file = '/some/world/accessible/nfs/import_queue.txt';
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14 my $admin_email = 'admin@yoursite.gov';
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15
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16 ## HELP
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17 my $usage=<<'ENDHERE';
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18 NAME:
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19 galaxy_import.pl
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20 PURPOSE:
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21 To queue files to copy to Galaxy user's FTP folder for subsequent import into Galaxy.
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22 INPUT:
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23 @ARGV : one or more paths to copy (by default, skip folders; see -r)
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24 -r|recurse : recursively copy folders
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25 -e|email <email> : your email is your Galaxy user ID; only required if $EMAIL is not defined
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26 NB: email is case sensitive, must be same as Galaxy login.
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27 OUTPUT:
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28 stderr : error/warning messages
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29 -dev : copy to Galaxy/Dev instead of Galaxy/JGI (for developers only)
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30 NOTES:
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31 - ONLY *WORLD* READABLE PATHS CAN BE COPIED
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32 - user's environment variable, $EMAIL, may be set to make the --email option unnecessary
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33 - the copied files must be preprocessed by the galaxy copy daemon, which runs every 2min
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34 - you must import the files into Galaxy within 1 month or they will be purged!
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35 ENDHERE
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36
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37 ## OPTIONS
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38 my ($help,$email,$recurse,$dev);
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39 GetOptions(
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40 'help' => \$help,
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41 'email=s' => \$email,
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42 'recurse' => \$recurse,
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43 'dev' => \$dev
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44 );
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45
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46 ## VALIDATE INPUT
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47 if (!@ARGV or $help) {
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48 print $usage;
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49 exit;
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50 }
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51 if ($email) {
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52 1;
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53 } elsif ($EMAIL) {
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54 $email=$EMAIL;
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55 } else {
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56 die("Either --email or environment variable \$EMAIL is required\n");
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57 }
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58 die("This doesn't look like a valid email: $email\n") unless $email =~ /^\S+@\w+\.\w+$/;
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59 die("Queue file, $queue_file, does not exist; please notify Galaxy administrator at $admin_email\n") unless -f $queue_file;
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60
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61 # VALIDATE PATHS
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62 my %paths=();
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63 foreach my $path (@ARGV) {
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64 $path = abs_path($path);
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65 if (-f $path) {
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66 if (exists($paths{$path})) {
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67 warn("Skipping duplicate file, $path\n");
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68 } else {
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69 $paths{$path}=1;
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70 }
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71 } elsif (-d $path) {
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72 if ($recurse) {
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73 if (exists($paths{$path})) {
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74 warn("Skipping duplicate folder, $path\n");
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75 } else {
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76 $paths{$path}=1;
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77 }
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78 } else {
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79 warn("Skipping folder, $path; use -r to process folders\n");
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80 }
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81 } else {
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82 warn("Invalid path, $path\n");
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83 }
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84 }
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85
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86 # APPEND QUEUE FILE
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87 my @paths=keys %paths;
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88 exit unless @paths;
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89 open(QUEUE, ">>$queue_file") or die($!);
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90 while (@paths) {
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91 my $path=shift @paths;
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92 print QUEUE join("\t", $email, $path),"\n";
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93 }
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94 close QUEUE;
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95 exit;
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96 __END__
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97 Copyright(c) 2011 US DOE Joint Genome Institute.
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98 Use freely under the same license as Galaxy itself.
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