> > I noticed the recent update to Galaxy that allowed users to put data on > the galaxy FTP server and then import it into their history. > > Would it be possible to use a similar mechanism to import data from the > galaxy host file system but not use an FTP daemon? In our case we we > would like to mount a volume to the galaxy file server and allow people > to cp or mv data into it and then be able to import the data into their > history. Have you looked into "Data Libraries" ? There is also an option to allow uploading files by a non-admin user. For details see the "# -- Data Libraries" section in the 'universe_wsgi.ini' file. Regards, Hans > For example, In the context of the example at > http://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP > could you set up a directory called > '/home/nate/galaxy_dist/database/localfs/' instead of > '/home/nate/galaxy_dist/database/ftp/' which contained email named > directories and the files in these in these would be available to import > via the upload UI? Or is it all tied into FTP? > > Thanks for any advice, > > Steve > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev

Steve Taylor wrote: > Hi Hans, > > We did have a look at this but couldn't get it to work. But will try again. Hi Steve, If there are problems with this method please do let us know so we can look in to it.

Hi Nate, >If there are problems with this method please do let us know so we can >look in to it. > >Your thoughts about using the FTP upload as you describe should work >fine. Unfortunately it is not written so generically, so you'll need to >set an FTP server name in the appropriate option in the config file >despite not having one, which will be displayed in the help text on the >upload form. However, this server name is not verified in any way and >can be any string. > I'm trying to set up a directory using FTP Upload (without an FTP server :-)) as discussed above. I added a test directory for the a user 'auser' ftp_upload_dir = /data/galaxy/ ftp_upload_site = localhost to the universe.ini We are using LDAP, so I set up a test directory called /data/galaxy/auser(a)molbiol.ox.ac.uk but having added a file in can't see anything in the FTP upload section or the 'Files uploaded via FTP' section even when 'auser' is logged in. Is there something else I need to do?

Thanks, Steve

>>> If there are problems with this method please do let us know so we can >>> look in to it. >>> >>> Your thoughts about using the FTP upload as you describe should work >>> fine. Unfortunately it is not written so generically, so you'll need to >>> set an FTP server name in the appropriate option in the config file >>> despite not having one, which will be displayed in the help text on the >>> upload form. However, this server name is not verified in any way and >>> can be any string. >>> >> I'm trying to set up a directory using FTP Upload (without an FTP server :-)) as discussed above. >> >> I added a test directory for the a user 'auser' >> >> ftp_upload_dir = /data/galaxy/ >> ftp_upload_site = localhost >> >> to the universe.ini >> >> We are using LDAP, so I set up a test directory called >> >> /data/galaxy/auser(a)molbiol.ox.ac.uk >> >> but having added a file in can't see anything in the FTP upload >> section or the 'Files uploaded via FTP' section even when 'auser' is >> logged in. >> >> Is there something else I need to do? > > This should be it - are you certain the email in Galaxy exactly matches > the email used in the directory name (it's case-sensitive)? Yes. > And this > may be a silly question, but are you running a new enough revision that > has the FTP Upload code? > I think so. Just to double check is there a definitive way I can tell? In ./tools/data_source/upload.xml <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>

Steve Taylor wrote: >> >> I think so. Just to double check is there a definitive way I can tell? In ./tools/data_source/upload.xml >> >> <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/> >> > > > So I got this to work by hacking basic.py. > > def visible( self ): > self.tool.app.config.ftp_upload_dir = '/data/galaxy' > self.tool.app.config.ftp_upload_site = 'localhost' > > I can now see my files in my user directory. What is the best part of the code to use log.warning() to see what's going on? How can tell if it is reading the ini file ok? Hi Steve, sorry for not getting back to you. I hadn't realized there was a question here when I originally skimmed the email. This can be done in lib/galaxy/config.py > My next question is based on permissions. It looks like galaxy has to own the file (as nobody in your example) to upload and remove it from the directory. I'd like to change it to be more forceful, which would allow galaxy to remove the file if group owned by nobody. What module/lines do this and what impact would such a change have? This would likely have to be done in the tools/data_source/upload.py file.

We are going to be working on more general methods to allow for local file uploads in typical lab environments like yours where Galaxy users have access to (at least part of) the local filesystem, which would hopefully make this less of a hack for you.