Mercurial > repos > pitagora > imp_exp
changeset 0:07d3e0871bb4 draft
Uploaded
author | pitagora |
---|---|
date | Wed, 09 Jul 2014 04:48:09 -0400 |
parents | |
children | 75dc30937969 |
files | imp_exp/export.pl imp_exp/export.xml imp_exp/link_path.pl imp_exp/link_path.xml |
diffstat | 4 files changed, 85 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<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} ${i.name} +#end for +</command> +<inputs> + <param name="symlink" type="select" display="radio" label="Copy or symlink files?"> + <option value="0">COPY the files so I may delete the files from Galaxy</option> + <option value="1">SYMLINK the files; I will not delete the files from Galaxy</option> + </param> + <param name="dest" type="text" size='120' value="/home/galaxy/galaxy-work/" label="Destination folder" help="Must be writable by Galaxy user" /> + <repeat name="files" title="Files to export"> + <param name="file" type="data" format="data" label="File"/> + <param name="name" type="text" size='20' value="" label="Name" /> + </repeat> +</inputs> +<outputs> + <data name="logfile" format="txt" /> +</outputs> +<help> +**What it does** + +This tool allows staff to export files from Galaxy to a specified NFS path. + +The destination folder must be writable by the Galaxy user. It is suggested that you create a folder ~/dropbox and chmod 777 it. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imp_exp/link_path.pl Wed Jul 09 04:48:09 2014 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/perl + +# INTERNAL USE ONLY! +# THIS TOOLS IS WRITTEN BASED ON link_path.pl FROM US DOE Joint Genome Institute. +# 2012-02-10 Yamanaka + +# THIS TOOL HAS BEEN DEPRECATED IN FAVOR OF THE galaxy_import.pl AND gcpd.pl METHOD +# WHICH DON'T REQUIRE SETTING METADATA MANUALLY FOR EACH FILE. + +use strict; +use File::Copy; + +# CONFIG +my @allowed_paths = ('/'); + +# ARGS +my ($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;
--- /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 @@ +<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>