If you want another option, I wrote a quick tool wrapper and bash script. It's a total hack but it works. * create two files server_copy.sh and server_copy.xml in <<GALAXYDIR>>/tools/data_source with the following content. * Add the following line somewhere in your tool_conf <tool file="data_source/server_copy.xml"/> Cheers Dennis ##################<<bash script server_copy.sh>> ######################(this is ridiculously simple and does NO error check or validation - I have pretty good users) #!/bin/sh cp $* ##################<<XML script>>###################### <?xml version="1.0"?> <tool name="Server Upload" id="server_upload"> <!-- This tool is used when the user needs to access files stored on galaxy's server without routing through the client machine--> <description></description> <command interpreter="bash">server_copy.sh $input $output </command> <inputs> <param name="input" type="text" area="true" size="2x200" label="Full path to source file" help="The file must be specified as the full path - i.e. /home/user.name/mydata/foo.bar"/> <param name="out_format" type="select" label="Output data type"> <option value="fasta">FASTA</option> <option value="fastqillumina">FASTQ Illumina (or other qual=64)</option> <option value="fastqsanger">FASTQ Sanger (or other qual=33)</option> <option value="sam">SAM</option> <option value="bed">BED</option> <option value="text">TXT</option> <option value="interval">Interval</option> </param> <param format="txt" name="fname" type="text" size="200" label="Enter a name for your file."/> </inputs> <outputs> <data format="text" name="output" size="200" label="Moved: ${fname.value} " > <change_format> <when input="out_format" value="fasta" format="fasta" /> <when input="out_format" value="fastqillumina" format="fastqillumina" /> <when input="out_format" value="fastqsanger" format="fastqsanger" /> <when input="out_format" value="sam" format="sam" /> <when input="out_format" value="interval" format="interval" /> <when input="out_format" value="bed" format="bed" /> <when input="out_format" value="text" format="text" /> </change_format> </data> </outputs> </tool> On Wed, Jun 30, 2010 at 11:01 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Non-admin users can upload directories of files as well as long as the admin has set the following config in universe_wsgi.ini: # The following can be configured to allow non-admin users to upload a directory of files. The # configured directory must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or sub-directories of files # contained in their directory. user_library_import_dir = <some directory on the Galaxy instance's file system> allow_library_path_paste = True
On Jun 30, 2010, at 8:35 AM, Michael Siebauer wrote:
Hmm but there is no way, for a user to upload (without copying) his files. Only the Admin User can create and fill data libraries, right?
Cheers, Michael
Am 30.06.2010 12:17, schrieb Dennis Gascoigne:
When you import to a library (uploading from preconfigured server
directory) there is an option "No" to not copy, and instead use in
place.
We played with this for a while then decided against it. moving the
source fileor editing it etc. can cause havoc.
Cheers
Dennis
On Wed, Jun 30, 2010 at 8:01 PM, Michael Siebauer
<michael_siebauer@eva.mpg.de> wrote:
Hi,
is there a way/module or data Library that allows users to access there
files WITHOUT the need of uploading them first? Cause our Galaxy instance is
running within the intranet, all files could be accessed straight via NFS.
Thx, Michael ;-)
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