Hello Alessandro,

I misunderstood the issue you were raising in your initial email, but now 
understand based on the information you've supplied below.  

When you use the "Upload a directory of files" option to upload files to a data 
library, all of the files in the directory are uploaded (there is currently no 
way to choose which files in the directory to upload and which files to 
ignore).  So in order to keep from uploading files more than once, the files 
that have been previously uploaded will need to be removed from the 
subdirectory.  This same behavior applies to the "Upload files from filesystem 
paths" option if the path is pointing to a subdirectory of files.

The ability to select which files to upload and which to ignore is an 
enhancement that we'll add to our development roadmap, but it may be a while 
before we can get to it.

Sorry for my initial misunderstanding on this, as well as the inconvenience 
this may cause.

Greg Von Kuster


On Oct 14, 2011, at 11:21 AM, alessandro albiero wrote:

> Dear Greg,
> 
> many thank for your help. I follow all your instruction but my problem is 
> always the same.
> Attache you can find 3 images where you can see the problem.
> 
> In the figure 1, I'm uploading the files from my folder using sym link. As 
> you can see in the figure 2 there is my file (all_homo.fa).
> After that I added a new file in my folder and when I upload again this 
> folder, all the files are reuploaded. See the figure 3, here you can see that 
> the file all_homo.fa is present 2 times and there is also a new sam file.
> 
> I'd like to avoid the duplications and upload only the new file not 
> previously uploaded.
> 
> Probably I'm doing something wrong but I am not able to understand what.
> 
> All the best
> 
> Alessandro
> 
> 2011/10/12 Greg Von Kuster <g...@bx.psu.edu>
> Allesandro,
> 
> Are your users making the correct selection in the Copy data into Galaxy? 
> select list?  If they choose "Link to files without copying into Galaxy" as 
> shown below, you should see the behavior you want.  The default selection is 
> "Copy files into Galaxy", so if they leave the default selection, copies of 
> the files will be made.
> 
> <upload.tiff>
> 
> On Oct 12, 2011, at 12:10 PM, alessandro albiero wrote:
> 
>> Dear Greg,
>> 
>> thank you for your answer. I followed the wiki but I did not solve my 
>> problem.
>> I setted these parameters on the universe_wsgi.ini:
>> 
>> user_library_import_dir = /u/galaxy/userimport
>> 
>> Then I created the /u/galaxy/userimport directory with a series of sub-dirs 
>> named as the login users. 
>> I done this to allow our user to load into galaxy their  files. In this case 
>> every user put its data in its dir on /u/galaxy/userimport (or using 
>> symlinks) and then load them on galaxy.
>> 
>> My problem is that galaxy duplicate the files; for example:
>> 
>> 1) User "A" place a file "FILE1" on its dir and it load the dir on galaxy. 
>> On galaxy he sees "FILE1"
>> 2) The user "A" place another file in its dir ("FILE2") and re-load the dir 
>> on galaxy. On galaxy he sees "FILE1", "FILE1", "FILE2" 
>> 
>> It seems that galaxy re-loads all the files of the user dir without checking 
>> the duplications.
>> We would like to avoid this duplications.
>> 
>> We found that removing the old files from the user directory solves the 
>> problem. Is there a simpler way to do this (without removing the files) ?
>> 
>> 
>> All the best
>> 
>> Alessandro
>> 
>> 
>> 
>> 2011/10/11 Greg Von Kuster <g...@bx.psu.edu>
>> Hello Alessandro,
>> 
>> You can upload files from filesystem paths to a Galaxy data library without 
>> copying the files into Galaxy's configured file directory.  This approach 
>> should provide what you're looking to do.  See our wiki at 
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files 
>> for all of the details.
>> 
>> Greg Von Kuster
>> 
>> On Oct 11, 2011, at 6:45 AM, alessandro albiero wrote:
>> 
>>> Dear all,
>>> 
>>> I have a problem with galaxy and I have already tried to write on ther user 
>>> list....
>>> My problem concern the upload on galaxy of new files.
>>> 
>>> We are setting up a galaxy istance on our server (HPC Cluster with torque 
>>> and PBS) for internal use.
>>> Our problem is that we manage only NGS data (SOLiD and Illumina Data) that 
>>> are already stored on the server. 
>>> We tried to set up the user directory in the universe_wgsi.ini file to 
>>> allow to any user tu upload their local files, but adding new file and 
>>> re-uploading the dir we found duplicated files (it seems that galaxy 
>>> re-upload every time all the files ignoring if some are already present). 
>>> This method is OK for us but how can we avoid the file duplications ?
>>> 
>>> In a presentation found on web (blankenberg_pittsburg_2001), we saw that 
>>> there is the possibility to automatically upload the sequenced reads on 
>>> Galaxy (and let them available to all our user). Where can we find 
>>> information for doing this ?
>>> 
>>> 
>>> Thank in advance
>>> 
>>> All the best 
>>> 
>>> Alessandro 
>>> 
>>> 
>>> 
>>> 
>>> --
>>> ******************************
>>> Alessandro Albiero
>>> Bioinformatics Lab
>>> CRIBI-Padua University
>>> Viale G. Colombo, 3
>>> 35121 Padova-Italy
>>> 
>>> http://genomics.cribi.unipd.it
>>> http://genomics.cribi.unipd.it/index.php/User:Albiero
>>> Phone. +39. 049 827-6165
>>> Fax.   +39. 049 827-6159
>>> ********************************
>>> 
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>>  http://lists.bx.psu.edu/
>> 
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
>> 
> 
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
> 
> 
> 
> 
> <Fig_1.png><Fig_2.png><Fig_3.png>

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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