[galaxy-user] Upload data to local Galaxy by copying them to the file folder

2012-10-12 Thread Jerzy Dyczkowski 

Hello,

How to put data to the local Galaxy server via ftp, ssh or copying 
directly to some subfolder in galaxy-dist?


We installed a local Galaxy instance and it is running. Manual uploading 
files from user PCs is slow due to less than perfect connections in the 
local network. We would prefer uploading large files by ssh from the 
central cluster to the server on which Galaxy is running. I can conect 
to the Galaxy server and Galaxy folder structure, however, I cannot find 
where to put files. Are they all renamed and coded as something like: 
galaxy-dist/database/files/000/dataset_38.dat ?


The option of uploading via ftp on main.g2.bx.psu.edu is absent in local 
Galaxy distribution.


best regards,

Jerzy
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[galaxy-user] cuffdiff values different for same sample

2012-10-12 Thread i b 
Hello forum,
I have ran cuffdiff with two samples, treated vs untreated, and had
certain values as expressed in the output (isoform differential
expression).

When I ran it again, using a different treated sample, but SAME
UNTREATED SAMPLE, the values assigned to the untreated are different.

Why is this if values are calculated from a unique FPKM? This happend
for other jobs where I have ran the same untreated vs other treated
samples...

Thanks a lot,
ib
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Re: [galaxy-user] Upload data to local Galaxy by copying them to the file folder

2012-10-12 Thread Jennifer Jackson 

Hi Jerzy,

To load data in batch on a local install, use the Data library function. 
The admin can do this and you can also grant permissions to specific 
users. Please see these wiki pages for details:


http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

The first is an overview, the second has details for various loading 
options, including through a file system. The idea is to load into a 
Data Library, then import into histories through the UI. There is no 
data duplication, it is done through references.


Hopefully this helps,

Jen
Galaxy team

On 10/12/12 5:04 AM, Jerzy Dyczkowski wrote:

Hello,

How to put data to the local Galaxy server via ftp, ssh or copying
directly to some subfolder in galaxy-dist?

We installed a local Galaxy instance and it is running. Manual uploading
files from user PCs is slow due to less than perfect connections in the
local network. We would prefer uploading large files by ssh from the
central cluster to the server on which Galaxy is running. I can conect
to the Galaxy server and Galaxy folder structure, however, I cannot find
where to put files. Are they all renamed and coded as something like:
galaxy-dist/database/files/000/dataset_38.dat ?

The option of uploading via ftp on main.g2.bx.psu.edu is absent in local
Galaxy distribution.

best regards,

Jerzy
___
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/


--
Jennifer Jackson
http://galaxyproject.org
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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:

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