# HG changeset patch
# User pitagora
# Date 1404897805 14400
# Node ID 4c225e57d44b3835c30f7e5c100481c0c46e0fa1
# Parent 75dc30937969b4bc8dc3abad4af164289098cf59
Uploaded
diff -r 75dc30937969 -r 4c225e57d44b export.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/export.pl Wed Jul 09 05:23:25 2014 -0400
@@ -0,0 +1,32 @@
+#!/usr/bin/perl
+
+use strict;
+use File::Copy;
+use File::Basename;
+
+# ARGS
+my ($symlink, $dest, $logfile, @files)=@ARGV;
+die("Absolute path required\n") unless $dest =~ /^\//;
+die("Paths containing '..' are disallowed\n") if $dest =~ /\/\.\.\//;
+die("Only /home/*, /house/*, and /ifs/* paths are allowed\n") unless $dest =~ /^\/home/ or $dest =~ /^\/house/ or $dest =~ /^\/ifs/;
+die("Destination folder does not exist: $dest\n") unless -e $dest;
+die("Destination path is not a folder: $dest\n") unless -d $dest;
+
+# CP
+open(OUT, ">$logfile") or die($!);
+while (@files) {
+ my $file=shift @files or die("Source filename required\n");
+ my $name=shift @files or die("Destination filename required\n");
+ print OUT "$file -> $dest/$name\n";
+ if ($symlink) {
+ symlink($file, "$dest/$name");
+ } else {
+ copy($file, "$dest/$name");
+ }
+}
+close OUT;
+print "Exported ", scalar(@files), " to $dest\n";
+exit;
+__END__
+Copyright (c) 2011 US DOE Joint Genome Institute.
+Use freely under the same license as Galaxy itself.
diff -r 75dc30937969 -r 4c225e57d44b export.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/export.xml Wed Jul 09 05:23:25 2014 -0400
@@ -0,0 +1,29 @@
+
+to a Local File
+export.pl $symlink $dest $logfile
+#for $i in $files
+${i.file} ${i.name}
+#end for
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool allows staff to export files from Galaxy to a specified NFS path.
+
+The destination folder must be writable by the Galaxy user. It is suggested that you create a folder ~/dropbox and chmod 777 it.
+
+
diff -r 75dc30937969 -r 4c225e57d44b link_path.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/link_path.pl Wed Jul 09 05:23:25 2014 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/perl
+
+# INTERNAL USE ONLY!
+# THIS TOOLS IS WRITTEN BASED ON link_path.pl FROM US DOE Joint Genome Institute.
+# 2012-02-10 Yamanaka
+
+# THIS TOOL HAS BEEN DEPRECATED IN FAVOR OF THE galaxy_import.pl AND gcpd.pl METHOD
+# WHICH DON'T REQUIRE SETTING METADATA MANUALLY FOR EACH FILE.
+
+use strict;
+use File::Copy;
+
+# CONFIG
+my @allowed_paths = ('/');
+
+# ARGS
+my ($src, $dest, $symlink)=@ARGV;
+die("Absolute path required\n") unless $src =~ /^\//;
+die("Paths containing '..' are disallowed\n") if $src =~ /\/\.\.\//;
+my $ok=0;
+foreach my $dir (@allowed_paths) {
+ my $re="^$dir";
+ $re =~ s/\//\\\//g;
+ if ($src =~ /$re/) {
+ $ok=1;
+ last;
+ }
+}
+die("Not an allowed source path\n") unless $ok;
+
+# CP
+unlink($dest);
+if ($symlink) {
+ symlink($src, $dest);
+} else {
+ copy($src,$dest);
+}
+exit;
diff -r 75dc30937969 -r 4c225e57d44b link_path.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/link_path.xml Wed Jul 09 05:23:25 2014 -0400
@@ -0,0 +1,18 @@
+
+a Local File
+link_path.pl $source $dest $symlink
+
+
+
+
+
+
+
+
+
+
+
+This tool allows you to import a local file into Galaxy.
+You have to edit the imported file's metadata to assign it to the appropriate datatype.
+
+