Hi,
I have installed the Picard tools using the Tool-shed functionality in
the admin tools.
The tools and requisites have been correctly installed and run correctly.
The insert statement to the event table fails however. I get the
following error on screen:
|OperationalError:
Hi,
I have implemented a custom tool called 'barcode-parse' and uploaded this
custom to into my local tool shed(which is running at http://localhost:9009).
Also able to install this custom tool from galaxy.
Then I have added simple repository dependency. I have created a xml file
Dear there,
When I used SnpEff in local galaxy instance, I got an error:
Exception in thread main java.lang.UnsupportedClassVersionError:
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method) at
Hi Xiaofei,
Dear there,
When I used SnpEff in local galaxy instance, I got an error:
Exception in thread main java.lang.UnsupportedClassVersionError:
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at
java.lang.ClassLoader.defineClass1(Native Method) at
Can you give us the complete error message. The important part is missing.
Here is the whole thing for the error:
Traceback (most recent call last):
File
/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py,
line 48,
Hi Xiaofei,
To get the complete error message, can you click on the bug icon (left-most
icon at the bottom of the expanded history item) of the error’d dataset and
copy and paste from the page that loads in the middle pane?
Thanks for using Galaxy,
Dan
On Apr 2, 2014, at 12:04 PM, Wang,
Oh, yes, here it is:
Traceback (most recent call last):
File
/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py,
line 48, in module
if __name__ == __main__: main()
File
Hi guys,
I keep getting an error everytime I start up the galaxy server. I am guessing
this has to do with a job that galaxy is trying to resume and cannot find.
galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking
active jobs
Traceback (most recent call last):
File
This looks very to similar to an issue discussed here:
http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html.
The default branch of Galaxy contains changeset that should address
this issue -
Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled
exception calling queue_job
Traceback (most recent call last):
File /opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 62, in run_next
John,
Thanks for this. I am new to managing galaxy, but how do I go about updating my
galaxy to reflect these changes? I found directions on
https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about
pulling changes from the bitbucket repository. Does this preserve my
When I used SnpEff in local galaxy instance, I got an error:
Exception in thread main java.lang.UnsupportedClassVersionError:
ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version
51.0 at java.lang.ClassLoader.defineClass1(Native Method) at
Hi,
that means that the snpeff annotation is missing. You can install it
with the snpeff datamanager under your Admin panel. Have a look at the
wiki page about data-manager and the snpeff wrapper documentation.
You do not need to edit xml files. If so that is an bug in the wrapper
and we
Hi Luca,
Are you passing any params to the runner for inclusion as PBS submit
parameters (param id=nativeSpecification in job_conf.xml)?
--nate
On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo lucato...@gmail.com wrote:
Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
Thanks Björn. Luca, what version of pbs-drmaa are you using now?
On Wed, Apr 2, 2014 at 2:40 PM, Björn Grüning bjoern.gruen...@gmail.comwrote:
Hi Nate,
I tried to help Luca today, but I failed totally ...
He is not using param id=nativeSpecification at all. Or put it that
way if he isn't
Dear Nate, and Björn
thankyou for your help. As Björn said, indeed i get always the same error
message regardless if I use the id=nativeSpecification or not. How can one
figure out the version of pbs-drmaa that the system is using ? It would be
really useful to have a step-by-step tutorial on how
Hi Luca,
We generally have not provided detailed documentation on this portion since
it's not really within the scope of Galaxy itself, and documentation would
be likely to become out of date as these external libraries (like
pbs-drmaa) are updated, and cluster configurations are very
Thankyou Nate for your prompt and detailed support.
Unfortunately I am on a different time zone and I do not have access now to
the system.
Thankyou for the suggestion you provided me to do the debugging.
I will carry that out in about 12 hours from now and let you know.
Thankyou again
Luca
p.s.
Hi Nate,
I tried to help Luca today, but I failed totally ...
He is not using param id=nativeSpecification at all. Or put it that
way if he isn't using it, he gets the same error.
Cheers,
Bjoern
Am 02.04.2014 20:34, schrieb Nate Coraor:
Hi Luca,
Are you passing any params to the runner for
Dear Bjoern,
As your suggestion, I tried to install the snpEff annotation. But, I think I am
still be stuck there. What I did is:
Admin Data Manage local data (beta), then the message is shown as below.
(For the BWA and Fetching genome, I installed them from tool_sheds by myself.
For the
Hey Mo,
Sorry for the super delayed response here. I can't find a decision to
remove it documented anywhere, so my guess is that this tool was
unintentionally removed when we last updated the volume. It's actually
still available on disk, though, and can be re-enabled in your
tool_conf.xml by
Hi Xiaofei,
Dear Bjoern,
As your suggestion, I tried to install the snpEff annotation. But, I think I am
still be stuck there. What I did is:
Admin Data Manage local data (beta), then the message is shown as below.
(For the BWA and Fetching genome,
I installed them from tool_sheds by
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the next
update of Cloudman?
Is there a protocol (or help page) available for how to re-enable tools in
the 'tool_conf.xml'? One of the great things about Galaxy Cloudman is that
someone who doesn't know programming
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote:
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the
next update of Cloudman?
I'll check to make sure there wasn't a good reason to remove it (couldn't
find one in my first pass, and it's
Hi all,
It seems that the recent release does not support label element anymore,
i.e. no sub-section with the section title displayed in grey. Is there any
alternative way to organize the tool under one big section?
Best regards!
Jun
This was kindly fixed by Nicola Soranzo
(https://bitbucket.org/galaxy/galaxy-central/pull-request/346/fix-for-https-trellocom-c-8npgym3u-1430/diff)
and merged into the latest stable branch of galaxy-central. There are
ongoing discussions internally about how to best get these between
release fixes
Hi Dannon,
Thanks so much, your protocol was extremely helpful!
Thanks for looking into ENA SRA. In our experience, the ENA SRA is the
easiest and most reliable way of importing public NGS data into Galaxy. The
ENA SRA has an actual button to click that will import your data set of
choice into
After SnpEff Databases Execute you still need to pick genome of
interest and run SnpEff Download. SnpEff Databases just downloads a
list of available genomes.
You mean SnpEff Download under Data Manager? But, there is no response when I
click on it.
Unfortunately, I tried to uninstall the
This change is very small and was not committed to the stable branch
of galaxy-central so I would just modify the your Galaxy's copy of the
pbs runner file directly until the next release:
% wget
https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0/raw
-O
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