Configuring Galaxy for FTP upload
Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.). Thank you in advance for any help. CL
On Apr 23, 2012, at 10:31 PM, Ciara Ledero wrote:
Hi all,
According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.).
Thank you in advance for any help.
Hi Ciara, ProFTPd is not required. If your Galaxy users already have a way to access the server directly, that access method is fine. You simply need to create a top-level directory under which you create directories for each user. Then, set the top level directory as the value of 'ftp_upload_dir' in the config file, and set 'ftp_upload_site' to something other than the default 'None'. e.g.: /scratch/galaxy/upload /scratch/galaxy/upload/user1@example.org /scratch/galaxy/upload/user2@example.org ftp_upload_dir = /scratch/galaxy/upload ftp_upload_site = server.example.org --nate
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Hi all, So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question: Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None. Thanks in advance for the help! Cheers. CL
On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote:
Hi all,
So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question:
Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None.
Hi Ciara, You only need to do this if you plan to allow users to upload files to their histories via FTP (or another file transfer mechanism). If you don't need this functionality, you don't need to configure it. --nate
Thanks in advance for the help!
Cheers.
CL
On Jun 11, 2012, at 9:10 AM, Nate Coraor wrote:
On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote:
Hi all,
So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question:
Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None.
Hi Ciara,
You only need to do this if you plan to allow users to upload files to their histories via FTP (or another file transfer mechanism). If you don't need this functionality, you don't need to configure it.
--nate
Nate, Were there plans to remove the 'FTP'-ness from this to indicate that any method for data transferal (sftp, scp, etc) works? chris
On Jun 11, 2012, at 3:45 PM, Fields, Christopher J wrote:
On Jun 11, 2012, at 9:10 AM, Nate Coraor wrote:
On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote:
Hi all,
So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question:
Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None.
Hi Ciara,
You only need to do this if you plan to allow users to upload files to their histories via FTP (or another file transfer mechanism). If you don't need this functionality, you don't need to configure it.
--nate
Nate,
Were there plans to remove the 'FTP'-ness from this to indicate that any method for data transferal (sftp, scp, etc) works?
chris
Yes, that's the plan. --nate
Another question, Nate. After running Galaxy, I had problems with accessing the data in the created upload folder. Is there anything else that I need to do? Thank you so much for all the help.
participants (3)
-
Ciara Ledero -
Fields, Christopher J -
Nate Coraor