Re: [galaxy-dev] upload from local filesysem

2012-05-23 Thread Bossers, Alex 
You can do so / allowing them to, by using the galaxy ftp solution.

That way users can link or provide files in their email subdirs. You have to 
sort out how to set the users/rights properly on your linux box though.

But see the galaxy ftp solution pages, it might be of help.

Alex


Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
namens J. Greenbaum [jgb...@liai.org]
Verzonden: woensdag 23 mei 2012 3:01
To: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] upload from local filesysem

It seems that this topic has been covered at least several times and I've found 
this thread to be helpful:

http://user.list.galaxyproject.org/Speed-up-uploading-into-local-Galaxy-terribly-slow-tp4429327p4436053.html

However, as far as I understand, this will only allow the Admin to do the 
upload from a local disk.  Has anyone had success allowing a regular user to 
upload from a local disk?  This seems like a common issue, particularly with 
large sequencing files.  It would be great to be able to add this as the first 
step in a workflow.

Any info would be appreciated.

Thanks,

Jason

--
Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgb...@liai.orgmailto:jgb...@liai.org
La Jolla Institute for Allergy and Immunology






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Re: [galaxy-dev] upload from local filesysem

2012-05-23 Thread J. Greenbaum 
Thanks for the reply. Ideally, I would have a cron job run that would monitor a 
directory and automatically add the new files to a particular library. I do not 
want the end users to have to deal with this. Does anyone have a working 
solution or ideas for implementation? This is the main sticking point that is 
preventing us from using galaxy for our in-house next-gen sequencing pipeline. 

Thanks, 

Jason 

-- Jason Greenbaum, Ph.D. 
Manager, Bioinformatics Core | jgb...@liai.org 
La Jolla Institute for Allergy and Immunology 

- Original Message -

 From: Alex Bossers alex.boss...@wur.nl
 To: J. Greenbaum jgb...@liai.org, galaxy-dev@lists.bx.psu.edu
 Sent: Wednesday, May 23, 2012 1:24:13 AM
 Subject: RE: [galaxy-dev] upload from local filesysem

 You can do so / allowing them to, by using the galaxy ftp solution.

 That way users can link or provide files in their email subdirs. You
 have to sort out how to set the users/rights properly on your linux
 box though.

 But see the galaxy ftp solution pages, it might be of help.

 Alex

 
 Van: galaxy-dev-boun...@lists.bx.psu.edu
 [galaxy-dev-boun...@lists.bx.psu.edu] namens J. Greenbaum
 [jgb...@liai.org]
 Verzonden: woensdag 23 mei 2012 3:01
 To: galaxy-dev@lists.bx.psu.edu
 Onderwerp: [galaxy-dev] upload from local filesysem

 It seems that this topic has been covered at least several times and
 I've found this thread to be helpful:

 http://user.list.galaxyproject.org/Speed-up-uploading-into-local-Galaxy-terribly-slow-tp4429327p4436053.html

 However, as far as I understand, this will only allow the Admin to do
 the upload from a local disk. Has anyone had success allowing a
 regular user to upload from a local disk? This seems like a common
 issue, particularly with large sequencing files. It would be great
 to be able to add this as the first step in a workflow.

 Any info would be appreciated.

 Thanks,

 Jason

 --
 Jason Greenbaum, Ph.D.
 Manager, Bioinformatics Core |
 jgb...@liai.orgmailto:jgb...@liai.org
 La Jolla Institute for Allergy and Immunology
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