Hi again,
I have an important update - I was incorrect about workflow transfer
between Galaxy instances and where to edit. In summary, it is important
to do the workflow editing up-front before the export, instead of after
import. I'll explain why.
While it is now possible to import workflows from other Galaxy instances
(any), once actually in that new instance, if that workflow contains
tools that are not in the new target instance, there is nothing that can
be done with it (editing or running will result in a server error). This
is a known open issue with the workflow developers.
So, when you plan to import into the public main Galaxy instance, you
will need to modify any workflow in the source instance before exporting
it to make certain that it only contains tools that are present in the
public main Galaxy instance. If a server error results from an imported
workflow, an unavailable tool present in the workflow is the most likely
root cause of the problem.
If you plan to import into a local or cloud instance, then you have the
choice of either modifying the workflow and/or adding all of the
workflow tools to your local/cloud instance, and then importing the
workflow. You do not import the workflow first as this will result in an
error - if it occurs, delete the workflow and import again after the
required tools are added.
Good question and I apologize for getting this detail incorrect in the
original reply.
Best,
Jen
Galaxy team
On 5/23/12 10:06 PM, Jennifer Jackson wrote:
Hello,
On 5/23/12 7:30 PM, shamsher jagat wrote:
I have uploaded files in citsrome/ Gunner Ratch lab Galaxy instances
which allow users to use their tool. I want to either share work flow
from these instances or atleast transfer FAstq files to penn state
open source galaxy severer. Is it possible or not?
Incorrect start -->>
It would not be possible to share a workflow between two Galaxy
instance using the built in "Share or Publish" methods, however, you
should be able to download a workflow from one Galaxy instance and
then "Upload or import workflow" into the public main Galaxy instance
(this button is on the "Workflow" home page). Please note that any
tools included in your workflow that were available in the other
instance, but that are not available on the public main Galaxy
instance, would not be functional, so the workflow will likely need to
be edited before use.
<< -- Incorrect end, see above
Moving FASTQ datasets from other instances should also be
straightforward - download, then upload these to the public main
Galaxy instance using FTP. If you are having trouble downloading
workflows or datasets, then the host Galaxy instance should be contacted.
I have another question in this regard when I tried to upload the
FASTq files via web link or FTP the job is never completed. I have
tried it couple of times. This problem is there from last couple of
months. Are there so me changes which have been implemented recently
which is not allowing me to upload the files. Indeed I have seen from
last month or so too many messages suggesting either Tophat job stuck
or job is not completed or unable to upload the file. I am not if all
tehse problems are related (storage) or not. Can someone from Galaxy
team advice.
At this time, there are no known issues with upload functions. If you
are having problems with URL data transfer from another Galaxy
instance (or really, any 3rd party source), you can try to download
the data locally to your desktop in a terminal prompt (as a test) with
the command:
% curl -O
'copied_link_location_from_dataset_history_or_workflow_or_other_URL'
If this is successful, then a load into Galaxy should be successful.
If this is unsuccessful, first contact the source to check if the data
is publicly accessible, as they may have advice about requirements
concerning user/passwords in the URL. Once that is worked out and a
URL load still fails, please submit a bug report from the problematic
load (leaving the error dataset undeleted in your history) and we will
examine.
The main public instance occasionally has brief server/cluster issues
that impacted jobs, but these are very small portion of the overall
volume of jobs processed, and a re-run is the solution. We do our best
to respond quickly as soon as a problem is detected.
Reported delays due to high usage volume is a different matter. The
public main Galaxy instance has substantial dedicated resources, but
there are times when we still get very busy. If your analysis needs
are urgent or your jobs are numerous, then a local or cloud instance
is the recommended alternative: http://getgalaxy.org.
To be clear, you had FTP upload processes that were started but never
completed? If so, the connection may be been interrupted. When this
occurs, an FTP client will allow you to restart an upload so that it
will begin again where it left off. To do this, re-establish the
connection first, then resume the transfer.
http://wiki.g2.bx.psu.edu/FTPUpload
Hopefully this addresses your concerns,
Jen
Galaxy team
___________________________________________________________
The Galaxy User list should be used for the discussion of
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using "reply all" in your mail client. For discussion of
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
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
___________________________________________________________
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/
