Hi Jeremy,
Thanks for you assistance. I would love to try your suggestions, but
Galaxy won't start anymore.
I have found the root cause of the problems: my home partition has
become too small, due to a fat 'job_working_directory'. I didn't expect
it to become so big (especially with tophat
This changeset is only in galaxy-central, at the moment, and not galaxy-dist.
You have a few options here:
Pull directly from -central to the revision indicated (though this means you
will be updating your instance to less thoroughly tested galaxy-central code):
hg pull -u -r 5013377e0bf7
Thanks a lot Dannon, for your reply.
But hg keeps saying following when I try to pull: abort: unknown
revision '5013377e0bf7'!
Is there any other way of manually getting it?
(Sorry, I'm not an expert on those new SCMs)
Sanjar.
On 11/13/2012 06:33 PM, Dannon Baker wrote:
Sanjar,
This is
GALAXY TOOL ERROR REPORT
This error report was sent from the Galaxy instance hosted on the server
127.0.0.1:7070
-
This is in reference to dataset id 13 from history id 6
Hi,
We are looking into ways to integrate galaxy into the workflows of users
at our cluster, with lots of NGS users running all and any kind of
analyses on their typically huge amounts of data. For this we use a
parallel file system, available on all compute nodes.
This file system,
This may be implemented, I believe some people run Galaxy on the cluster,
but if not:
Galaxy normally operates on files stored in the database/files folder. If
your Galaxy instance has access to the files you need on your parallel fs,
I guess you could start by writing a tool that creates links
Hi Jorrit, thanks for the input!
On 11/14/2012 03:12 PM, Jorrit Boekel wrote:
This may be implemented, I believe some people run Galaxy on the cluster,
Yes, but AFAIK, most cluster job runners use some kind of file staging
(copying) into local storage on the compute nodes OR, require you do
Hi Joachim,
It looks like your integrated_tool_panel.xml file has been corrupted somehow.
You can move this file to a backup location (or delete) and it should be
automatically regenerated on Galaxy startup. If this fixes the issue, could you
share a copy of the file? It might be helpful for
Hi Rolando,
Please keep all replies on list.
Without a little more information its hard to guess what is happening. Can you
provide the log output for when you try to start the server?
Is this a cloud instance? If I had to make a guess, it would be that there is a
permissions problem due to
Hi Samuel
Have you looked at Data Libraries ?
(http://wiki.galaxyproject.org/Admin/Data%20Libraries/Libraries )
also look at the configurations in universe_wsgi.ini:
library_import_dir
user_library_import_dir
allow_library_path_paste
which gives you many option to access data out side of the
Make sure that you are pulling from galaxy-central and not galaxy-dist.
I believe something like:
hg pull -r rev# -u http://bitbucket.org/galaxy/galaxy-central
should work. The problem may be that you are pointing to galaxy-dist by
default, which will not know about that revision (yet).
-Scott
*Galaxy November 14, 2012 Distribution News Brief
http://wiki.galaxyproject.org/News/2012_11_14_DistributionNewsBrief*
*
Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14
*
*Highlights:*
*
*NGS: Picard (beta)* have moved from the *Galaxy distribution
Hello,
I am using the Galaxy public server to conduct a join operating on genomic
intervals. However, my job has not completed in over 2 days. Is there a
bug, and what can I do to speed up the process?
Thank you,
George
___
Please keep all
Hi
I apologize for abusing the list for a job add:
We are looking for a R/Bioconductor person which is familiar with Galaxy to
help us expanding our sets of NGS tools in Galaxy, see
http://www.fmi.ch/Careers/JobDetails.html?jobID=158
Please feel free to contact me for more details
Regards,
Dear Galaxy Devs,
I have tried to upload 2 files though the ftp upload using FileZila. I
have been getting the following error:
Response: 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP)
[:::128.118.250.4]
Command:USER **
Response: 331 Password required for
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