Hi,
the four processes I saw where all called "lastz" and ran in parallel and
consumed 100% of a core each.
My guess is that the lastz_wrapper.py is responsible for this.
Looking at it I see a some code regarding queuing and in the very beginning
this line:
WORKERS = 4
and further one the cla
Andreas,
I am not sure if you can call these "surprises".
Some tools (which I highly appreciate) of Peter have been "parallelised" to get
the job done more quickly. I earlier mentioned the ncbi blast+ wrappers but
there the tool by itself handles the multithreading.
Other tools I am aware that us
On Tue, Nov 27, 2012 at 8:58 AM, Andreas Kuntzagk
wrote:
> Hi,
>
> the four processes I saw where all called "lastz" and ran in parallel and
> consumed 100% of a core each.
> My guess is that the lastz_wrapper.py is responsible for this.
> Looking at it I see a some code regarding queuing and in t
Dear Peter,
As the author of several tool wrappers, I've been asking for a Galaxy
wide mechanism for Galaxy to tell the tool how many threads it can
use, for example via an environment variable. The value could then
be set with a general default, per runner default, or even per tool
using the ex
Hi Alex,
I am not sure if you can call these "surprises".
Well at least it surprised me :-)
Didn't want to sound to negative.
Some tools (which I highly appreciate) of Peter have been "parallelised" to get
the job done more
quickly. I earlier mentioned the ncbi blast+ wrappers but there the
On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
wrote:
> Dear Peter,
>
>> As the author of several tool wrappers, I've been asking for a Galaxy
>> wide mechanism for Galaxy to tell the tool how many threads it can
>> use, for example via an environment variable. The value could then
>> be set w
On Tue, Nov 27, 2012 at 10:44 AM, Andreas Kuntzagk
wrote:
> Hi Alex,
>
>> I am not sure if you can call these "surprises".
>
> Well at least it surprised me :-)
> Didn't want to sound to negative.
>
>> Some tools (which I highly appreciate) of Peter have been "parallelised"
>> to get the job done
Hi Peter,
thanks for your replies.
On 27.11.2012 11:44, Peter Cock wrote:
On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
wrote:
Dear Peter,
As the author of several tool wrappers, I've been asking for a Galaxy
wide mechanism for Galaxy to tell the tool how many threads it can
use, for e
Hi all,
This is a strange error, still lingering around on our Galaxy. From time
to time, some tools fail, with the same error:
job stderr:
/bin/sh: fastx_clipper: command not found
So I log in as the user Galaxy, and run the tools successfully on the
commandline. The solution is to restart
Hi,
In the past I installed bwa_wrapper from the toolshed. Unfortunately I must have choosen a wrong
category. Currently it is not part of any tool section. According to integrated_tool_panel.xml it's
supposed to be part of this section:
while it contains another section with the same name
Please ignore this. You can move it to a different section.
Andreas
On 27.11.2012 13:19, Andreas Kuntzagk wrote:
Hi,
In the past I installed bwa_wrapper from the toolshed. Unfortunately I must
have choosen a wrong
category. Currently it is not part of any tool section. According to
integrate
Dear Greg and Nikhil,
We just installed a local instance of galaxy and encountered the same problem as
Nikhil for the tools we tried to install from toolshed. Unfortunately I am not
skilled as you are and didn't manage to solve the problem from the information
in your posts.
In my case I have in
Hi,
What I remember is that while the lastz had died the python wrapper was still hanging around for
these 2 days. Maybe it's related to this builtin scheduler of the lastz wrapper.
Unfortunately I don't have time now to reproduce the error conditions.
regards, Andreas
On 26.11.2012 15:47, Bo
Hello Fab,
What version of Galaxy are you running? Did you install it from the
galaxy-dist repo on bitbucket? Am I understaning correctly that you are using
a symbolic link to point your installation directory to
/var/lib/galaxy-server/shed_tools? If so, why not just set the config setting
On Nov 27, 2012, at 6:06 AM, Andreas Kuntzagk
wrote:
> Hi Peter,
>
> thanks for your replies.
>
> On 27.11.2012 11:44, Peter Cock wrote:
>> On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
>> wrote:
>>> Dear Peter,
>>>
As the author of several tool wrappers, I've been asking for a Gal
On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko wrote:
>
> The "Right Way (TM)" I believe would be to have a universal resource request
> selector that could be plugged into any wrapper simply by including an
> appropriate element like say .
> Those variables could be exported, so the corres
On Nov 27, 2012, at 9:37 AM, Peter Cock wrote:
> On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko
> wrote:
>>
>> The "Right Way (TM)" I believe would be to have a universal resource request
>> selector that could be plugged into any wrapper simply by including an
>> appropriate element l
On Nov 20, 2012, at 8:15 AM, Peter Cock wrote:
> On Thu, Nov 15, 2012 at 11:21 AM, Peter Cock
> wrote:
>> On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock
>> wrote:
>>> On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock
>>> wrote:
Hi all,
Something has changed in the job handling, and
I went down something of a rabbit hole last night, I thought that
uploading files through the API using multipart/form-data worked. It
is only at the very end of my adventure that I realized it only works
for libraries uploads. I think it would be great to get that working
to histories as well. I c
On Tue, Nov 27, 2012 at 4:50 PM, Nate Coraor wrote:
> On Nov 20, 2012, at 8:15 AM, Peter Cock wrote:
>>
>> Is anyone else seeing this? I am wary of applying the update to our
>> production Galaxy until I know how to resolve this (other than just
>> be disabling task splitting).
>
> Hi Peter,
>
> T
On Nov 27, 2012, at 12:03 PM, Peter Cock wrote:
> On Tue, Nov 27, 2012 at 4:50 PM, Nate Coraor wrote:
>> On Nov 20, 2012, at 8:15 AM, Peter Cock wrote:
>>>
>>> Is anyone else seeing this? I am wary of applying the update to our
>>> production Galaxy until I know how to resolve this (other than j
Hi Harris,
I can't pin-point your issue exactly, to be honest I don't quite
remember how I got to this working configuration. Still please take a
look at this configuration as I'm using it in almost exactly the same
enviroment, Centos 6/Apache 2.2.15/Active Directory...
ServerAdmin admin@loc
Ilya,
Could you send me a failing input file, and I'll try to find out what is
failing?
Thanks,
JJ
--
Message: 6
Date: Tue, 27 Nov 2012 07:22:30 +
From: "Sytchev, Ilya"
To: "galaxy-dev@lists.bx.psu.edu"
Subject: [galaxy-dev] No output from IGVtools tile
M
Here's a link to one of the WIG files I am using:
https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip
I'd appreciate any pointers.
Thanks,
Ilya
On 11/27/12 3:57 PM, "Jim Johnson" wrote:
>
>
>
>Ilya,
>
>Could you send me a failing input file, and I'll try to find out what is
>failing
On Tue, Nov 27, 2012 at 5:19 PM, Nate Coraor wrote:
>>
>> So a little defensive coding could prevent the segfault then (leaving
>> the separate issue of why the jobs lack this information)?
>
> Indeed, I pushed a check for this in 4a95ae9a26d9.
Great. That will help.
>> This was a week ago, but
Ilya,
I fixed the igvtools_tile.xml tool config and pushed it to the toolshed.
Thanks for finding and reporting the problem.
JJ
On 11/27/12 3:18 PM, Sytchev, Ilya wrote:
Here's a link to one of the WIG files I am using:
https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip
I'd appreciat
The error is gone, thank you very much! What was the problem?
Ilya
On 11/27/12 5:34 PM, "Jim Johnson" wrote:
>Ilya,
>I fixed the igvtools_tile.xml tool config and pushed it to the toolshed.
>Thanks for finding and reporting the problem.
>JJ
>
>On 11/27/12 3:18 PM, Sytchev, Ilya wrote:
>> Here
Hello,
Thanks to everyone for the feedback and suggestions. I was eventually
able to puzzle out what was going awry. The remaining issues turned out
to be:
1) When proxying was enabled, to trigger an authentication request with
the default Galaxy set-up, I needed to use the “localhost” URL,
Hi,
I am trying to run SICER (version 0.0.1) in galaxy to call peaks using the
galaxy interface browser. My workflow is as follows. First I uploaded BAM files
of my ChIP tag and input tag data, I then convert these to SAM files with the
SAMtools tool, and then convert the SAM files to intervals
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