atada
for example.
Cheers,
Bjoern
Am 19.11.2014 um 10:36 schrieb Peter Briggs:
Hello
I'm trying to make a new repository on the public toolshed at
https://toolshed.g2.bx.psu.edu/
but I keep getting the "internal server error" page.
I was also unable to log out, or even to see
lse having this problem?
Thanks & best wishes
Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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esn't surprise me that Galaxy can handle certain
parameters changing between versions but not conditionals - they are
handled in a much more complex manner. I have updated this
(https://trello.com/c/INCluhxP) Trello card to reference this problem.
Sorry I don't have better news right now.
-Jo
eated?
Thanks, best wishes
Peter
Ps this is in galaxy-dist changeset 14355:007f6a80629a
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Ple
issue i.e. the "KeyError: 'platform' exception when I
have the two versions of this tool installed from a local toolshed, and try
switching between to the newer one from the older one.)
Any help or suggestions are greatly appreciated.
Many thanks
Peter
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Peter Briggs peter.b
sts
to get the newer behavior. This fixes a lot of problems.
The older runner will also not accept the syntax but the newer runner
should no problem.
Hope this gives you some ideas on how to proceed.
-John
On Wed, Sep 17, 2014 at 5:37 AM, Peter Briggs
wrote:
Hello all
I'm experiencin
ki.galaxyproject.org/TestingInstalledTools
so I'm wondering if anyone can point out what it is that I'm missing. No
doubt it's blindingly obvious, but I just can't see it.
Thanks again for any help
Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core
ine 1910, in
submit_form
for value in kwd[ control.name ]:
KeyError: 'operations_0|operation|name'
Is there a way to specify the the value in the tests? I've tried both
and
in my s, but neither form seem to change the exception from the tests.
Any sugge
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
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Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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output in the tool directory. I've felt with the naming
convention requited by Galaxy and the tool works from the command line.
I know that the issue isn't with my local Galaxy install because a
generic tool I've installed that produces multiple outputs works fine.
I've attached my c
.
Should it be possible to do what I'm trying? Or is there a different way
to do it?
Thanks for any help or suggestions,
Best wishes
Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
_
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files
(bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing
bowtie's stderr output and adding it as an additional history item (here the
?
-Greg
On Wed, Feb 27, 2013 at 4:21 AM, Peter Briggs
wrote:
Hello Greg
It looks like you're running the version of the MACS14 tool from the
toolshed? I think we also ran into this here and I patched the
macs14_wrapper.py thusly to work around it:
diff --git a/macs14/macs142_wrapper.p
ace at:
http://lists.bx.psu.edu/
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Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
--- bowtie_wrapper.xml 2013-02-19 16:34:58.172013341 +
+++ bowtie_wrapper_fls.xml 2013-02-19 16:39:
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Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility Univer
ile.
>> 2. GATK2 works on Galaxy but I did something wrong on installing it.
>>
>> Could anyone help me about this? It will be greatly appreciated.
>>
>> Thanks.
>>
>> Anthonel ___
>> Please ke
rt than the actual Galaxy server, of course).
And you have a real-time overview how busy the Galaxy server is, who is
doing what, and (hopefully not) what errors occur. And at the end of the
day or month you get your stats.
Regards, Hans-Rudolf
On 12/05/2012 12:04 PM, Peter Briggs wrote:
Hello
The
t the reports in a browser running on localhost, shut it down again as
required) but does anyone run it in a more persistent set-up? Or is
ad-hoc the way to go?
Any suggestions welcome, many thanks
Best wishes, Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Fac
ally, is there a way to keep the locally defined datatypes
separate from the main
datatypes_conf.xml file?
Thanks for any advice or comments (& apologies if I've missed anything
obvious on the list or on the wiki)
Best wishes, Peter
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Peter Briggs peter.bri...@manchester.ac.uk
Bioinfo
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McManus for the original fix.)
Best wishes, Peter
On 16/10/12 16:36, Peter Briggs wrote:
Hello
I've encountered an error when creating the first data library within a
Galaxy installation.
The data library appears to be created but an error message appears
("Error attempting to displa
a new data library on an
instance which already has existing libraries, and debug output doesn't
give me any additional clues about where the "missing module" is coming
from.
I don't think this problem has been reported previously however
apologies if it's alread
n your mail client. To manage your subscriptions to this
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Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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for some time in the next week or so, so you can
wait for it if you want.
Sorry for the inconvenience!
Greg Von Kuster
On Apr 23, 2012, at 5:53 AM, Peter Briggs wrote:
Hello
I've encountered some problems installing and then trying to remove a tool from
the main toolshed in a loca
quot;Manage installed tool shed
repositories".
We're using the most recent galaxy-dist (hg reports our most recent
changeset as 6799:40f1816d6857).
I don't know if anyone else has encountered this problem but it would be
useful to know how to either complete the a
ns doesn't currently have sections for bfast:
https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
I'd be happy to add some details there if that would help (I'm pjbriggs
on bitbucket, and it seems to allow me edit privileges on the wiki?).
Thanks & best wishes
Peter
ated and has the right column values but
still isn't showing up, you've got another issue. Do you have a
tool_data_table_conf.xml file that contains an entry for
"bfast_indexes"? Let us know if you are still having issues.
Thanks,
Kelly
On Thu Jun 23, at 12:11 PM, Peter
hanged wrt this issue in Galaxy Central), or if I've missed
something really obvious.
Thanks for your help, best wishes
Peter
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