Mercurial > repos > pitagora > imp_exp
changeset 1:75dc30937969 draft
Deleted selected files
author | pitagora |
---|---|
date | Wed, 09 Jul 2014 04:48:40 -0400 |
parents | 07d3e0871bb4 |
children | 4c225e57d44b |
files | imp_exp/export.pl imp_exp/export.xml imp_exp/link_path.pl imp_exp/link_path.xml |
diffstat | 4 files changed, 0 insertions(+), 85 deletions(-) [+] |
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--- a/imp_exp/export.xml Wed Jul 09 04:48:09 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -<tool id="export" name="Export" version="1.0.0"> -<description>to a Local File</description> -<command interpreter="perl">export.pl $symlink $dest $logfile -#for $i in $files -${i.file} ${i.name} -#end for -</command> -<inputs> - <param name="symlink" type="select" display="radio" label="Copy or symlink files?"> - <option value="0">COPY the files so I may delete the files from Galaxy</option> - <option value="1">SYMLINK the files; I will not delete the files from Galaxy</option> - </param> - <param name="dest" type="text" size='120' value="/home/galaxy/galaxy-work/" label="Destination folder" help="Must be writable by Galaxy user" /> - <repeat name="files" title="Files to export"> - <param name="file" type="data" format="data" label="File"/> - <param name="name" type="text" size='20' value="" label="Name" /> - </repeat> -</inputs> -<outputs> - <data name="logfile" format="txt" /> -</outputs> -<help> -**What it does** - -This tool allows staff to export files from Galaxy to a specified NFS path. - -The destination folder must be writable by the Galaxy user. It is suggested that you create a folder ~/dropbox and chmod 777 it. -</help> -</tool>
--- a/imp_exp/link_path.pl Wed Jul 09 04:48:09 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -#!/usr/bin/perl - -# INTERNAL USE ONLY! -# THIS TOOLS IS WRITTEN BASED ON link_path.pl FROM US DOE Joint Genome Institute. -# 2012-02-10 Yamanaka - -# THIS TOOL HAS BEEN DEPRECATED IN FAVOR OF THE galaxy_import.pl AND gcpd.pl METHOD -# WHICH DON'T REQUIRE SETTING METADATA MANUALLY FOR EACH FILE. - -use strict; -use File::Copy; - -# CONFIG -my @allowed_paths = ('/'); - -# ARGS -my ($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;
--- a/imp_exp/link_path.xml Wed Jul 09 04:48:09 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<tool id="import" name="Import" version="1.0.0"> -<description>a Local File</description> -<command interpreter="perl">link_path.pl $source $dest $symlink</command> -<inputs> - <param name="source" type="text" size='100' value='' label="Complete pathname" /> - <param name="symlink" type="select" display="radio" label="Is that a permanent location?"> - <option value="0">No, COPY the file</option> - <option value="1">Yes, SYMLINK the file</option> - </param> -</inputs> -<outputs> - <data format="data" name="dest" /> -</outputs> -<help> -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. -</help> -</tool>