12:22 p.m.
Hi,
I'm trying to download multiple files from a given history but I couldn't
figure out how to do it.
Is there a way?
Thanks,
Adhemar
2:22 p.m.
Hello Adhemar,
There are two current choices:
1 - Use "Options -> Export to File". This will export the entire
history, which can then be loaded into your own local copy of Galaxy (or
any other Galaxy instance that you have access to) for review. If you
only want portions of a particular history, first copy those items into
a new history ("Options -> Copy Datasets"), then export the history for
that limited set.
2 - Click on the disc icon for each dataset that you want to download
and save. You should be able to queue up a few overlapping download
processes at the same time. When overlapping, this will slow them down,
but you won't need to wait for one to finish, then start the next, and
so forth.
If you find that the downloads are failing due to large data size(s),
you can try unix tools such as wget or curl. This will work for both
exported histories and individual datasets. For histories, the link is
provided, so that can be directly copied. For datasets, right click on
the disc icon and use "Copy Link Address.". Then use this syntax:
% wget '<link>'
or
% curl -O '<link>'
Hopefully one of these options will work out for you,
Best,
Jen
Galaxy team
On 1/17/12 9:22 AM, Adhemar wrote:
Hi,
I'm trying to download multiple files from a given history but I
couldn't figure out how to do it.
Is there a way?
Thanks,
Adhemar
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7:37 p.m.
New subject: cuff... errors
Hi,
Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job output not
returned by PBS: the output datasets were deleted while the job was running, the job was
manually dequeued or there was a cluster error.
is there a system issue or something with my data?
r
8:30 p.m.
New subject: cuff... errors
Hi all,
FYI, I've gotten the same error recently when trying to run Bowtie (using
Galaxy Main).
Jeremy
On Tue, May 1, 2012 at 4:37 PM, Richard Mark White <whiter3(a)yahoo.com>wrote:
Hi,
Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job
output not returned by PBS: the output datasets were deleted while the job
was running, the job was manually dequeued or there was a cluster error.
is there a system issue or something with my data?
r
___________________________________________________________
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/
8:58 p.m.
New subject: cuff... errors
There was a temporary cluster issue, but it looks like jobs are running again. Try
resubmitting your jobs now, and they should succeed.
-Dannon
On May 1, 2012, at 8:30 PM, Jeremy Coate wrote:
Hi all,
FYI, I've gotten the same error recently when trying to run Bowtie (using Galaxy
Main).
Jeremy
On Tue, May 1, 2012 at 4:37 PM, Richard Mark White <whiter3(a)yahoo.com> wrote:
Hi,
Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job output not
returned by PBS: the output datasets were deleted while the job was running, the job was
manually dequeued or there was a cluster error.
is there a system issue or something with my data?
r
___________________________________________________________
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/
___________________________________________________________
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/
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galaxy-user@lists.galaxyproject.org
4 comments
5 participants
participants (5)
-
Adhemar -
Dannon Baker -
Jennifer Jackson -
Jeremy Coate -
Richard Mark White