# HG changeset patch
# User pitagora
# Date 1404895689 14400
# Node ID 07d3e0871bb4ecd72cc84987d9c490bc2e47afea
Uploaded
diff -r 000000000000 -r 07d3e0871bb4 imp_exp/export.pl
Binary file imp_exp/export.pl has changed
diff -r 000000000000 -r 07d3e0871bb4 imp_exp/export.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imp_exp/export.xml Wed Jul 09 04:48:09 2014 -0400
@@ -0,0 +1,29 @@
+
+to a Local File
+export.pl $symlink $dest $logfile
+#for $i in $files
+${i.file} ${i.name}
+#end for
+
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+**What it does**
+
+This tool allows staff to export files from Galaxy to a specified NFS path.
+
+The destination folder must be writable by the Galaxy user. It is suggested that you create a folder ~/dropbox and chmod 777 it.
+
+
diff -r 000000000000 -r 07d3e0871bb4 imp_exp/link_path.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imp_exp/link_path.pl Wed Jul 09 04:48:09 2014 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/perl
+
+# INTERNAL USE ONLY!
+# THIS TOOLS IS WRITTEN BASED ON link_path.pl FROM US DOE Joint Genome Institute.
+# 2012-02-10 Yamanaka
+
+# THIS TOOL HAS BEEN DEPRECATED IN FAVOR OF THE galaxy_import.pl AND gcpd.pl METHOD
+# WHICH DON'T REQUIRE SETTING METADATA MANUALLY FOR EACH FILE.
+
+use strict;
+use File::Copy;
+
+# CONFIG
+my @allowed_paths = ('/');
+
+# ARGS
+my ($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 000000000000 -r 07d3e0871bb4 imp_exp/link_path.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imp_exp/link_path.xml Wed Jul 09 04:48:09 2014 -0400
@@ -0,0 +1,18 @@
+
+a Local File
+link_path.pl $source $dest $symlink
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+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.
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+