Re: [galaxy-dev] workflow problems

2016-07-28 Thread Cristel Thomas
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] dataset collection datatype

2016-07-29 Thread Cristel Thomas
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

[galaxy-dev] workflow problems

2016-07-27 Thread Cristel Thomas
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

[galaxy-dev] Writing test for dataset collection

2016-07-11 Thread Cristel Thomas
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

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

2016-07-11 Thread Cristel Thomas
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

Re: [galaxy-dev] error on startup

2016-09-01 Thread Cristel Thomas
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

[galaxy-dev] error on startup

2016-09-01 Thread Cristel Thomas
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

Re: [galaxy-dev] error on startup

2016-09-01 Thread Cristel Thomas
> 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

Re: [galaxy-dev] Problem downloading HTML datasets

2016-09-14 Thread Cristel Thomas
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] multiple datatypes input in 16.07

2016-12-13 Thread Cristel Thomas
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

2016-12-14 Thread Cristel Thomas
of 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 <cristel.tho...@gmail.com> wrote: > Hey Sam, > thanks, I'll check tomorrow at work b

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

2016-12-14 Thread Cristel Thomas
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

2016-12-14 Thread Cristel Thomas
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

2016-12-05 Thread Cristel Thomas
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: >

[galaxy-dev] multiple datatypes input in 16.07

2016-12-05 Thread Cristel Thomas
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] multiple datatypes input in 16.07

2016-12-05 Thread Cristel Thomas
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

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

2016-12-05 Thread Cristel Thomas
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

[galaxy-dev] jupyter notebook / nginx / ssl

2017-05-30 Thread cristel thomas
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