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. 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 <greg@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 ********************************

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

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