[galaxy-dev] jupyter notebook / nginx / ssl

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

Re: [galaxy-dev] New datatypes with code dependencies

at 4:16 PM, Björn Grüning <bjoern.gruen...@gmail.com> 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 datat

[galaxy-dev] New datatypes with code dependencies

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

Re: [galaxy-dev] multiple datatypes input in 16.07

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

Re: [galaxy-dev] multiple datatypes input in 16.07

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: >

Re: [galaxy-dev] multiple datatypes input in 16.07

ther words, Galaxy > will 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 <cristel.tho...@gmail.com> > wrote: > >> Hi Sam, >> I'm not sure

Re: [galaxy-dev] multiple datatypes input in 16.07

you can reproduce the error on usegalaxy.org? Does it happen > for all tools? > > Thanks, > Sam > > On Mon, Dec 5, 2016 at 8:47 AM, Cristel Thomas <cristel.tho...@gmail.com> > wrote: > >> Hi Galaxy Devs, >> >> We have a few tools with multip

[galaxy-dev] multiple datatypes input in 16.07

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

Re: [galaxy-dev] Problem downloading HTML datasets

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

Re: [galaxy-dev] error on startup

mar...@bx.psu.edu> wrote: > 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 <cristel.tho...@gmail.com> > wrote: > >> Hi Martin, >> th

Re: [galaxy-dev] error on startup

> what `host` 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 <cristel.tho...@gmail.com> > wrote: > >> Galaxy admins, >&g

[galaxy-dev] error on startup

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

[galaxy-dev] dataset collection datatype

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

Re: [galaxy-dev] workflow problems

t; This is indeed weird behavior. What revision is your Galaxy at? >>> >>> On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas <cristel.tho...@gmail.com >>> <javascript:_e(%7B%7D,'cvml','cristel.tho...@gmail.com');>> wrote: >>> >>>> Hi all, >&

[galaxy-dev] workflow problems

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

Re: [galaxy-dev] Writing test for dataset collection

u have further questions. The documentation regarding this > is a still bit scarce, I am sorry. > > Martin > > On Mon, Jul 11, 2016 at 3:24 PM Cristel Thomas <cristel.tho...@gmail.com> > wrote: > >> Dear galaxy developers, >> >> Can someone point me