enabling regular users to upload large data volumes to a local Galaxy server
Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
FTP server. Ilya -----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Yury V Bukhman Sent: Monday, November 14, 2011 3:01 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Perhaps someone else will find this of interest. As it turned out, we didn't need FTP for a local server. Instead, one can set an option in universe_wsgi.ini (or universe_wsgi.webapp.ini if you are running multiple web server processes) to allow regular users to upload a set of files from a file system into a data library. Thus we have set up a drop box on a shared drive, with a subfolder for each user, where they can put their files, and gave each user their own data library in Galaxy where those files can be uploaded. The drop box folder is mounted on the Galaxy server. The option in universe_wsgi.webapp.ini is: user_library_import_dir = /mnt/dropbox It seems to work... Yury On 11/14/2011 5:25 PM, Chorny, Ilya wrote:
FTP server.
Ilya
-----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Yury V Bukhman Sent: Monday, November 14, 2011 3:01 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server
Hi,
we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated.
Thanks.
Yury
-- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman@glbrc.wisc.edu
participants (2)
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Chorny, Ilya -
Yury V Bukhman