Dear Nate, dear Peter
Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If
I try to get the data out of the library into anothre history, I am
successful for the html but not for the blastdb. The problem seems to be
that the primary data file
Hi Geert
A simple solution might be: you hand over a string containing all three
paths to your wrapper, and then the wrapper splits the string into the
three individual paths.
Hans-Rudolf
On 07/27/2014 04:44 PM, Geert Vandeweyer wrote:
Hi,
I'm working on tool wrapper that needs three
If I understand you correctly, would this mean generating a custom .loc
file for this tool containing the concatenated paths? Or can I
concatenate paths from different .loc files somehow, which would allow
me to use the default loc files?
Geert
On 07/28/2014 09:33 AM, Hans-Rudolf Hotz wrote:
On 07/28/2014 10:02 AM, Geert Vandeweyer wrote:
If I understand you correctly, would this mean generating a custom .loc
file for this tool containing the concatenated paths? Or can I
concatenate paths from different .loc files somehow, which would allow
me to use the default loc files?
This
On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer wrote:
> Dear Nate, dear Peter
>
> Sorry for the delay in replying.
>
> I can import both HTML and blastdb from a history to a data library. If
> I try to get the data out of the library into anothre history, I am
> successful for the html but not for
Dear all,
I noticed that with params of type "text" Galaxy seems to replace
certain characters before passing them to the shell. As examples, it
changes "@" to "__at__", "}" to "__cc__" and "\" to "X".
Is this the standard behavior or am I doing something wrong ? And if
it's standard, are ther
Hi,
I use labels as subsection separators in my too_conf.xml. Now, I use a
local tooshed and I wonder if there is a way to declare such a labels
for tools installed from my toolshed sot that the tool will be in the
selected section with a label as subsection separator?
Thanks.
Yec'han
==
On Mon, Jul 28, 2014 at 11:03 AM, Wolfgang Maier
wrote:
> Dear all,
>
> I noticed that with params of type "text" Galaxy seems to replace certain
> characters before passing them to the shell. As examples, it changes "@" to
> "__at__", "}" to "__cc__" and "\" to "X".
> Is this the standard behavio
On 28.07.2014 12:22, Peter Cock wrote:
This is standard behaviour to prevent special characters being used
to construct malicious command lines. It can be configured within
your tool definition using the tag set:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_
On Mon, Jul 28, 2014 at 12:23 PM, Wolfgang Maier
wrote:
> On 28.07.2014 12:22, Peter Cock wrote:
>>
>> This is standard behaviour to prevent special characters being used
>> to construct malicious command lines. It can be configured within
>> your tool definition using the tag set:
>>
>> https://
On 28.07.2014 13:32, Peter Cock wrote:
On Mon, Jul 28, 2014 at 12:23 PM, Wolfgang Maier
wrote:
On 28.07.2014 12:22, Peter Cock wrote:
This is standard behaviour to prevent special characters being used
to construct malicious command lines. It can be configured within
your tool definition usin
Hi Hans-Rudolf.
Yes, I have this error in my log file :"MySQL server has gone away"!!!
So I changed the option database_engine_option_pool and it seems to work fine!
Thanks a lot for your help.
And for the information, when a job is queued on a local instance not
in a cluster, when we restart th
We are having issues with using Galaxy in Internet Explorer 11 (these work fine
in Chrome & Firefox).
1. The jobs queued and history doesn't display unless you refresh the
browser window. Clicking the history reload icon doesn't work.
2. If I click to edit something in the history
Hi Dori,
the IE is not really supported. There are many issues with IE and it's
hard to deal with that. If possible please you Chrome or FF, both are
supported and tested.
Cheers,
Bjoern
Am 28.07.2014 um 16:40 schrieb Sajdak, Doris:
We are having issues with using Galaxy in Internet Explore
Hi, Dori
Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs
in the history panel now, but in the meantime:
- can you open the javascript console in your IE and see if any errors are
displayed when doing the two tasks you mention?
http://msdn.microsoft.com/en-us/library/ie/b
Hi Carl & Dori,
sorry for the misinformation, for some reason I thought the official
statement was that IE is not supported.
Thanks for clarification!
Bjoern
Am 28.07.2014 um 16:54 schrieb Carl Eberhard:
Hi, Dori
Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs
in t
There's an as-yet undocumented method that you can use to get arbitrary fields
in a loc file:
__get_data_table_entry__(, , ,
)
So for the novoalign entry you could do:
--novoidx ${__get_data_table_entry__(‘novoalign’, ‘dbkey’, $input.dbkey,
‘path’)}
Finally, I like your indexing syntax, and
Hi All,
I am having problems using GATK Indel Realigner. We installed our own galaxy
instance on a VM server and configured it to submit jobs through DRMAA to the
clusters.
The first error I got is:
"
ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK
Key file.
Excellent, thanks !
Geert
On 07/28/2014 05:02 PM, Jeremy Goecks wrote:
There's an as-yet undocumented method that you can use to get
arbitrary fields in a loc file:
__get_data_table_entry__(, , ,
)
So for the novoalign entry you could do:
--novoidx ${__get_data_table_entry__(‘novoalign’,
Hi,
Is there a known issue in the latest galaxy-dist related to displaying
txt files? If I click the eye icon for a 'txt' dataset, nothing is
shown. The preview shows the data correctly, and if I check the path on
the server, the data and contents are definitely there.
main.log doesn't show
Hi all,
I'm working with data_collection as type of input in xml files. but I
use all the datasets of a collection to compute some results that I
want to push in a "data_collection" output.
I know how take each dataset of a data_collection input with my
script, like this :
...
for $f in $input
...
Hi Carl,
Thanks for the help. Here’s what I get when I try to upload a new file:
SCRIPT438: Object doesn't support property or method 'attachEvent'
File: jquery.js, Line: 1514, Column: 3
SCRIPT5009: 'jQuery' is undefined
File: jquery.migrate.js, Line: 6, Column: 2
SCRIPT5009: 'jQuery' is undefin
Dear sir
I was trying to use the DDBJ pipeline for the high level analysis I was
trying to use P-Galaxy but I am not able to upload the data from DDBJ
pipeline
--
With Regards
Lakshmi.K
M.S(By Research)
Anna University
Chennai- 44
___
Ple
Discard this, it appears to be solved after changes to htaccess files on
our server.
On 07/28/2014 05:30 PM, Geert Vandeweyer wrote:
Hi,
Is there a known issue in the latest galaxy-dist related to displaying
txt files? If I click the eye icon for a 'txt' dataset, nothing is
shown. The prev
24 matches
Mail list logo
