Hi Luca,
I think we have a nice feature for you:
https://wiki.galaxyproject.org/UserDefinedToolboxFilters
Thanks for using Galaxy,
Bjoern
Am 19.02.2014 08:54, schrieb Luca Toldo:
dear Galaxians,
the users of my galaxy service are quite eterogenous, and would like
to have the toolbar customis
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster wrote:
> Hi Peter,
>
> We'll try to get some time to look at your tool_dependencies.xml recipe as
> soon as possible.
>
> Greg Von Kuster
>
>
Hi Greg,
Overnight this has gone back to the previously observed missing
data problem (e.g. email of 4t
Hi Geert,
I tried to update the R package to include the libpng dependency, if you
like to test it ...
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_0_2
Do you know if cairo is really needed? If I can I would omit to have a
dependency on cairo :)
Cheers,
Bjoern
Hi all,
I instal
Hi all,
I'm looking for examples of tools which take multiple input
files (one or more, determined at run time) and produce
multiple output files (one for each input file). Any
specific suggestions?
I have a number of sequence filtering/renaming tools
where this might be useful - in some cases ta
Hi all,
I was recently wondering how it might be possible for
an output from tool A to be used as a parameter when
calling tool B (without modifying tool B to take a data
configuration file or anything like that).
To clarify, I'm thinking about simple parameters like
a single integer/float/string
Hey Peter,
Have you seen this solution?
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
It always seems to get mentioned when this topic is brought up. It has
serious limitations in terms or workflow running, but
Dear all,
I don't have an instance of galaxy that manages sequencing requests. I would
like to, but I would like to know a single thing: Is the interface friendly
enough to make me define multiple sample at once in a single request?
Thanks
d
___
On Wed, Feb 19, 2014 at 2:16 PM, John Chilton wrote:
> Hey Peter,
>
> Have you seen this solution?
>
> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
>
> It always seems to get mentioned when this topic is brought
On Wednesday, February 19, 2014, Peter Cock
wrote:
> On Wed, Feb 19, 2014 at 2:16 PM, John Chilton
> >
> wrote:
> > Hey Peter,
> >
> > Have you seen this solution?
> >
> >
> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_
Hi Shenwiyn,
Can you specify what is not working? Did you find the file?
Thanks,
Sam
On Wed, Feb 19, 2014 at 1:42 AM, shenw...@gmail.com wrote:
> Hi Sam and Hans-Rudolf，
> Thank you very much for your help.It seems that the
> static/scripts/galaxy.menu.js fail to work in my local Galaxy.As a
>
Dear all,
I don't have an instance of galaxy that manages sequencing requests. I would
like to, but I would like to know a single thing: Is the interface friendly
enough to make me define multiple sample at once in a single request?
Thanks
d
___
FYI: it is my understanding that such tools cannot be used in a workflow at
this time.
On Feb 19, 2014 10:08 AM, "Carlos Borroto" wrote:
> On Wednesday, February 19, 2014, Peter Cock
> wrote:
>
>> On Wed, Feb 19, 2014 at 2:16 PM, John Chilton
>> wrote:
>> > Hey Peter,
>> >
>> > Have you seen th
> On Feb 19, 2014 10:08 AM, "Carlos Borroto" wrote:
>>
>> Hi Peter,
>>
>> I used the current functionality here:
>> http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode
>>
>> The code for the underlining tool is available here:
>> https://github.com/cjav/ngs-tools
>>
>> Hope it helps,
>> Carlo
Hello Tobias,
Thanks for the heads up. I am not sure what the best way to address
this is - but if I still was responsible for a public server I think I
would open my datatype_conf.xml file and replace all instances of
"application/xml" and "image/svg+xml" with "text/plain" in an effort
to get G
Hello Davide,
yes it does.
Also these two modifications of Galaxy might be if an interest to you as
they enhanced the sample tracking further:
http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/
http://bioinformatics.oxfordjour
On Wed, Feb 19, 2014 at 11:04 AM, Peter Cock wrote:
> On Wed, Feb 19, 2014 at 3:33 PM, Michael Crusoe
> wrote:
>> FYI: it is my understanding that such tools cannot be used in a workflow at
>> this time.
>
> That would be a problem :(
Well, I haven't checked but I don't see why it would be a pro
I suggested augmenting the tool_conf syntax as part of the DataCollection
development.
To replace the need for the the multiple output determined at runtime,
I suggest being able to declare data collections within the outputs tags, and
being able to use regular expressions in the from_work_di
Hello,
In my tool UI, I have a select tool as follows:
Localhost
Midway
UC3
Stampede
Tukey
How do I tell it to preselect value "localhost" by default?
Currently, user has to explicitly select the a value but if she for
Hi Ketan,
You can specify "selected=true"[1]
[1]
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coption.3E_tag_set
On 19 February 2014 20:14, Ketan Maheshwari wrote:
> Hello,
>
> In my tool UI, I have a select tool as follows:
>
>
> Localhost
>
Great! Thanks.
On Wed, Feb 19, 2014 at 2:18 PM, Saket Choudhary wrote:
> Hi Ketan,
>
> You can specify "selected=true"[1]
>
> [1]
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coption.3E_tag_set
>
>
> On 19 February 2014 20:14, Ketan Maheshwari
> wrote:
> > Hello,
> >
> > In
hi,
The dependencies installed fine, but R itself gave this error:
configure: error: unrecognized option:
`-I/galaxy/galaxy_tool_binaries/libpng/1.6.7/devteam/package_libpng_1_6_7/a0b0e0281cc4/include'
Try `./configure --help' for more information
Any idea what might be wrong?
Best,
Geert
Hello Peter,
Please see below…
On Feb 19, 2014, at 4:41 AM, Peter Cock wrote:
> Hi Greg,
>
> Overnight this has gone back to the previously observed missing
> data problem (e.g. email of 4th Feb) - no test results at all:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
>
> Te
On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster wrote:
>
> Hello Peter,
> Please see below...
>
> ...
>
> Your above email arrived in my inbox at 4:42 AM EST, and
> it looks like your repository in question was not yet tested.
Ah. That would partly explain things - perhaps coupled with
a cache
Hi Peter,
Dave B and I just discovered that issue that causes your tests to fail.
The problem lies with our current implementation supporting the
action tag, which is used in your recipe. This tag
ultimately uses Python's os.listdir via shutil.move.
It turns out that certain Python version
On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> Dave B and I just discovered that issue that causes your tests to fail.
>
> The problem lies with our current implementation supporting the
> action tag, which is used in your recipe.
> This tag ultimately uses Python's os.li
Hi Geert,
can you retest please, I had a typo. Unfortunately, I can't test it by
myself since my internet connection is to bad here in Slovenia to
download that R-tarball.
Sorry,
Bjoern
hi,
The dependencies installed fine, but R itself gave this error:
configure: error: unrecognized opti
Hi Peter,
On Feb 19, 2014, at 6:09 PM, Peter Cock wrote:
> On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> Dave B and I just discovered that issue that causes your tests to fail.
>>
>> The problem lies with our current implementation supporting the
>> action tag,
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