Dear galaxy developers,
Can someone point me to a resource explaining how to write the test section
of the xml for tools dealing with dataset collections? as input as well as
output.
Thanks much,
Cris
___
Please keep all replies on the list
The documentation regarding this
> is a still bit scarce, I am sorry.
>
> Martin
>
> On Mon, Jul 11, 2016 at 3:24 PM Cristel Thomas
> wrote:
>
>> Dear galaxy developers,
>>
>> Can someone point me to a resource explaining how to write the test
>> section
Hi all,
I ran into a weird behavior on my local instance of galaxy and I was
wondering if anyone had the same experience (and if so what did you do to
fix it?).
When trying to run a workflow by clicking on the workflow name, it works.
When trying to run the workflow by clicking on the arrow next t
>>
>> On Wed, Jul 27, 2016 at 10:06 PM, Dannon Baker > > wrote:
>>
>>> This is indeed weird behavior. What revision is your Galaxy at?
>>>
>>> On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas >> > wrote:
>>>
>>>> Hi all,
Hello galaxy developers,
how do you set the format for datasets in output dataset collections? I
looked at some xmls from John Chilton, and tried using
format_source="input", or inherit_format="true". Those unfortunately do not
work. I also naively tried format="txt" to no avail.
I can't find any
Hi Bjorn,
here's what I have:
I tried this among other things:
I'll try your example. Thank you!
On Fri, Jul 29, 2016 at 3:21 PM, Björn Grüning
wrote:
> Hi Cristel,
>
> can you share some code. If you use discover_datasets like this,
> format="" should indeed wo
Galaxy admins,
One of you has probably seen the below error before, can someone explain?
for background, we're running our instance on a AWS server (if that makes a
difference)
galaxy.web.framework.base DEBUG 2016-05-19 12:43:40,545 Enabling
'sample_tracking' controller, class: SampleTracking
gal
t` and `port` is in your reports.ini config file? This stacktrace
> would point at something already running at the same port.
>
> Martin
>
> On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas
> wrote:
>
>> Galaxy admins,
>> One of you has probably seen the below error b
e:
> Cris: please check whether some previous instance of Reports isn't still
> running and/or check your ports using e.g. `netstat`
> M.
>
> On Thu, Sep 1, 2016 at 1:19 PM Cristel Thomas
> wrote:
>
>> Hi Martin,
>> the config is:
>> port = 8081
>&
Not that helpful, but we have the same problem with our 16.04 instance.
On Tue, Sep 13, 2016 at 10:21 AM, Stephanie LE GRAS
wrote:
> Hi there,
>
>
>
> I’m currently facing several problems with the galaxy instance I’m
> managing. I’m going to send a mail per problem so sorry in advance : for
> f
Hi Galaxy Devs,
We have a few tools with multiple datatypes as input. They work fine in
16.01. In 16.07 though, the selection of files in the tools' drop-downs
include every single file in the history, instead of just the files from
the specified data types.
Anyone else run into this? Any idea of
oduce the error on usegalaxy.org? Does it happen
> for all tools?
>
> Thanks,
> Sam
>
> On Mon, Dec 5, 2016 at 8:47 AM, Cristel Thomas
> wrote:
>
>> Hi Galaxy Devs,
>>
>> We have a few tools with multiple datatypes as input. They work fine in
>> 16
l implicitly convert the fasta file to a tabular file and present it as
> a valid option in the select field.
>
>
>
> On Mon, Dec 5, 2016 at 11:48 AM, Cristel Thomas
> wrote:
>
>> Hi Sam,
>> I'm not sure what tools have multiple datatypes as input on usegalaxy
If it's implicit conversion, why does it pick up the FCS bianry format
along with the other text formats?
and why does it get triggered on every single tool instead of just the few
that have the multiple datatypes?
On Mon, Dec 5, 2016 at 12:31 PM, Aysam Guerler
wrote:
> Ok, so this seems to work
Hey Sam,
thanks, I'll check tomorrow at work but I suspect there might be something
else - I use rpy2 to call R, so that FCS files can be read. As of 2 months
ago there was no efficient way of doing it strictly in python. rpy2 does
not load if R isn't installed on the system (and for this specific
f the implicit conversion?
I would love some input on what you guys think we should do about adding
the FCS datatype to Galaxy.
Thanks again,
Cris
On Tue, Dec 13, 2016 at 8:52 PM, Cristel Thomas
wrote:
> Hey Sam,
> thanks, I'll check tomorrow at work but I suspect there might be some
Hello,
We'd like to add some datatypes to Galaxy specific to flow cytometry
(finally). One of the datatype is a binary format which requires rpy2/R to
be read (no good python module available to do that).
How do you guys deal with that?
Thanks,
Cris
___
On Wed, Dec 14, 2016 at 4:16 PM, Björn Grüning
wrote:
> Hi Cristal,
>
> Am 14.12.2016 um 22:07 schrieb Cristel Thomas:
> > Hello,
> >
> > We'd like to add some datatypes to Galaxy specific to flow cytometry
> > (finally). One of the datatype is a binary for
Hi Galaxy developers,
we are trying to get notebooks to run on our production server, with half
success: we can get jupyter to load, and it does access the history, but
notebooks uploaded to history do not load, and any modification to the
notebook provided can be saved but do not show up when the
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