Thanks Carlos, I will give it a look over and see what works best for my
situation. I think for my first demo setup, I am going to create an SGE
environment in my ESX cluster, and just test out the main galaxy server
/ SGE head, with 3-4 baby nodes.
AC
On 06/21/2012 11:25 AM, Carlos Borroto wrote:
On Thu, Jun 21, 2012 at 8:54 AM, Alan V. Cowles <alan.cow...@duke.edu> wrote:
My first question: Is there a way to make the galaxy server retrieve data
from a local storage set, instead of uploading newly through the web
interface? Http seems like an awfully inefficient way to transmit sequence
data. If I mounted an nfs directory full of sequence to the server could I
load and analyze it, and what options would I do to config this?
I would highly recommend to take a look at the admin documentation on
Galaxy's Wiki[1]. You do have several options to upload data from a
local file system and share it with your users using Data
Libraries[2]. You can also configure your Galaxy to allow users to use
FTP to upload data[3], this can also be easily adapted to any other
method by which your users can place the data in the specify directory
in Galaxy's config( I personally prefer using scp or rsync over ssh,
as all my users have local unix account in the server.)
[1]http://wiki.g2.bx.psu.edu/Admin
[2]http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
[3]http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP
My second question: When setting up a cluster do most people make the galaxy
server a head and farm out to compute nodes, or do you send jobs off to a
remote cluster entirely? It seems like the options in the universe_wsgi.ini
file calls a local daemon for cluster management, but I am a bit confused.
My Galaxy server happens to run on my SGE head node, but as long as
the node running Galaxy has qsub abilities and ideally share a file
system with the cluster, you should be fine. There is a way around the
shared file system but I haven't used so far. You can find
documentation about both options in Galaxy's Wiki[4].
[4]http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
Hope it helps,
Carlos
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