Hello Dannon,
Thanks for resolving the issue of snpEff HTML display. It's working well with
the new changeset. But the gene file link in the bottom
(dataset_*.dat.genes.txt) is still in broken state, says could not find file.
Any update on this?
-Raj
-Original Message-
From:
Hello everyone,
I wanted to start the drmaa job runner and followed the instructions in
the wiki, but I have this error message when I start Galaxy:
galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable:
galaxy.jobs.runners. drmaa
Traceback (most recent call last):
File
Dear all,
How do I get the new Galaxy look enabled that you see in
usegalaxy.org? I have two servers on the latest galaxy-dist.
regards,
Leandro
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Dear all,
Is it normal that the latest galaxy-dist creates a shed_tools
directory one directory up (and outside) from the server galaxy-dist
directory?
best,
Leandro
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Dear All,
If i browse (outsode of Galaxy) to e.g.
http://www.ebi.ac.uk/ena/data/view/SRP001343 , and click on the Galaxy links
on that page, it used to be that the file got uploaded to my section of the
public Galaxy instance.
This was probably a bug instead of a feature, as currently it
Hi Anne,
We're aware that many tests require certain local data to be set up beforehand.
As such, these tests can't really be run at a local site. As part of
relocating our tools to the tool shed, we hope to fix this issue.
Thanks,
--nate
On Feb 20, 2012, at 1:25 PM, Anne Pajon wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f', u'
http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db',
I would like to get some idea about 'database_engine_option_pool_size' and
'database_engine_option_max_overflow' settings. We seem to hit both of these
limits whenever a user runs a large workflow with following error:
{{{
TimeoutError: QueuePool limit of size 40 overflow 50 reached,
Hi Leandro,
The directory should not have been created upon Galaxy server start-up. This
issue has been resolved in change set 6892:6b8535e5b030 in our central
repository. Thanks for reporting this.
Greg Von Kuster
On Mar 26, 2012, at 5:57 AM, Leandro Hermida wrote:
Dear all,
Is it
Hi Carlos,
Currently I am in a transition period, and I didn't get much time to look
on the same, Sorry for the delay.
For getting the read count, we wrote script and which is wrapped in Deseq
main program.
regards,
--Vipin T S
On 26 March 2012 14:01, Carlos Borroto carlos.borr...@gmail.com
Thanks for the update.
I wonder if when you had the time to upload your script to the
toolshed, you could use a different name from just plain DESeq to
avoid confusion. A researcher might expect a DESeq tool to use a read
count table and not BAM files as input.
Kind regards,
Carlos
On Mon, Mar
Hi Rocco,
To help us get oriented, which galaxy-dist pull did you start from and
which did you update to? If you have the release date/hg pull numbers,
that would be great. If you need to reference, these are the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs
Ideally, you
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