Problem solved: I found this stack trace in the job runner's log:
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in
command.run()
File
"/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run
invoke(command, command
Shashi,
I guess you are looking for the tool configuration XML options?
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
I guess its needless to say that you can only do this on your own instance of
galaxy locally.
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-de
Hi All,
I need the tool command in code file and want to change the command . is
there any way to change the command which is given under command tag .
Reagrds
shashi shekhar
___
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i
Hi All,
Sorry for the delay, I have had a couple of other projects on the go.
Still no good. I have made the data type unsniffable and added what I thought
was the correct information. I have also added the extension (sfx) to the list
of unsniffable binary formats in binary.py but it does not m
hi,
I can run galaxy in foreground on a mac just fine. However galaxy won't
run in daemon mode. galaxy main page doesn't load, and I get no errors.
Thanks.
-Sohail___
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in your mail c
Hi,
I'm a newbie when it comes to this kind of thing, so I was wondering whether
you can tell me the most appropriate place to ask questions about making some
modifications to your nglims extension for galaxy? Should they be posted to the
normal galaxy development list? Should I ask you directl
Yeah, and I fixed it... somehow.
In the lib/galaxy/web/form_builder.py I added the import on
string_as_bool from galaxy.util, then I modified the code as follows:
126 @staticmethod
127 def is_checked( value ):
128 if value == True:
129 return True
130 # This
Shantanu,
see dev-list mails of for instance May 16th. Deals with tools without input.
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Shantanu Pavgi [pa...@uab.edu]
Verzonden: maandag 23 mei 2011 18:30
Aan: gal
Hi again,
Very sorry to ask again, just gotten no repsonse, but is this a Galaxy bug
or does anyone have a functioning tool that takes multiple datasets as an
input parameter??? i.e.
regards,
Leandro
On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida wrote:
> Hi again,
>
> I tried changing the
Hi,
I am writing a simple tool (env command!) for debugging environment/path
related issues. Attached below is the xml config file. I noticed that inputs
tag is necessary for getting 'execute' button. Is there any way to execute
commands that have no input file/data? Also, can we have a simila
2011/5/23 Louise-Amélie Schmitt :
> @ Peter: I'm not sure I can get more precise... the checked attribute has no
> effect whatsoever, the boxes are always unchecked when I open the tool. I
> tried the "yes" and the "true" values to no avail.
>
> @ Leandro: Yes I already saw that ...
>
> But that's
@ Peter: I'm not sure I can get more precise... the checked attribute
has no effect whatsoever, the boxes are always unchecked when I open the
tool. I tried the "yes" and the "true" values to no avail.
@ Leandro: Yes I already saw that and tried to correct the code the way
someone suggested in
I am looking at options to configure settings such as wall-time, memory, and
number of cores etc. for each tool and wondering if this can be done using
multiple cluster job runner configurations. Is it possible to define multiple
cluster job runner configurations for each tool? In the universe
Ah right. Overlooked the shortcut EMPTY <>
Just not my way of doing it..
Alex
Van: Vipin TS [vipin...@gmail.com]
Verzonden: maandag 23 mei 2011 17:39
Aan: Bossers, Alex
CC: Jayant Khopale; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Need help with uploa
Hi Alex,
Indeed looking at the script it should be possible to use it as Vipin
> indicated.
> However, for xml validity I wouldn't use the 'naked' > or < signs but use
> > instead.
>
>
Thanks for pointing it.
> I am curious though on the script. Is it part of a larger script? Don't see
> any
Indeed looking at the script it should be possible to use it as Vipin
indicated.
However, for xml validity I wouldn't use the 'naked' > or < signs but use >
instead.
I am curious though on the script. Is it part of a larger script? Don't see any
ARGs being read from command line but may
On Mon, May 23, 2011 at 3:09 PM, Anton Nekrutenko wrote:
> Dear Peter:
>
> Yes, that would help.
One possibility would be to have all new bugs CC'd to the dev
mailing list? Not sure if everyone here would like that or not...
> But, you patches are definitely not unnoticed. We'll apply them
> (li
Not everything works correctly with checkbox booleans, the bug a couple
people and I reported long ago
https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional
is still there.
2011/5/23 Peter Cock
> 2011/5/23 Louise-Amélie Schmitt :
> > Hello,
> >
> > I
Dear Peter:
Yes, that would help. But, you patches are definitely not unnoticed. We'll
apply them (likely at the conference) and we are also in the process of
devising a strategy for doing so quickly and consistently.
See you on Tuesday.
a.
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://u
On Mon, May 16, 2011 at 8:59 PM, Spunde, Alex wrote:
> Same thing:
>
> [aspunde@ilmnhw-biolin10 galaxy-dist]$ python ./scripts/fetch_eggs.py
> Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
> Fetched
> http://eggs.g
Hi all,
I filled the following bugs 2 weeks ago, with patches:
https://bitbucket.org/galaxy/galaxy-central/issue/537/
Filter data on any column tool casts unused columns
https://bitbucket.org/galaxy/galaxy-central/issue/536/
Filter data on any column tools shows nonsense % vs total on stdout
ht
I have had good success in setting up a load balanced configuration
with nginx except that I get the following error when accessing Admin
-> Manage jobs:
"This Galaxy instance is not configured to run jobs. If using multiple
servers, please directly access the job running instance to manage
jobs."
2011/5/23 Louise-Amélie Schmitt :
> Hello,
>
> I know this is still not fully implemented and that there has already been a
> lot of messages on the topic, but I just would like to know if there's a way
> to make the "checked" attribute in the param tags have the required effect.
It might help if
Hello,
I know this is still not fully implemented and that there has already
been a lot of messages on the topic, but I just would like to know if
there's a way to make the "checked" attribute in the param tags have the
required effect.
Regards,
L-A
PS: looking forward to seeing the confere
I have also been getting such messages and even saying there are too
many re-bounces so your account is being disabled and I can not reactivate
using the link sent in email
On Sun, May 22, 2011 at 11:28 PM, shashi shekhar wrote:
>
>
> -- Forwarded message --
> From:
> Date: Mon,
Hi Jayant,
FYI the error still persists.
>
>
Please find the modified tool configuration file, attached here.
Just redirected your tool output to the result file in the below line
allsnp_modified.pl $input > $output
HTH, Vipin
for each sequence in a file
allsnp_modified.pl $input > $output
Hi,
Thanks! I have removed the white spaces. I am actually a beginner in Perl so
kindly bear with me. However I have one doubt, could it be because of the
usage of the redirection operator used in the usage of the perl script?
Kindly let me know. Regards.
On Mon, May 23, 2011 at 3:16 AM, Vipin TS
FYI the error still persists.
On Mon, May 23, 2011 at 3:36 AM, Jayant Khopale wrote:
> Hi,
>
> Thanks! I have removed the white spaces. I am actually a beginner in Perl
> so kindly bear with me. However I have one doubt, could it be because of the
> usage of the redirection operator used in the u
Hi Jayant,
Hi,
>
> I am trying to upload a Perl script into Galaxy however it gives me an
> error "*TypeError: 'NoneType' object does not support item assignment*".
> It seems that there is a mismatch between the input and output arguments and
> the file formats specified. I would really be thank
Hi,
I am trying to upload a Perl script into Galaxy however it gives me an error
"*TypeError: 'NoneType' object does not support item assignment*". It seems
that there is a mismatch between the input and output arguments and the file
formats specified. I would really be thankful if someone can he
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