Re: [galaxy-dev] History refresh in multi-thread mode and concurrent access

Hi, Christophe Just a note: I'm taking a look at this and seeing if I can reproduce the problem. Thanks for being patient. Carl On Tue, Sep 6, 2016 at 11:18 AM, Christophe Caron wrote: > Hi > > we run a Galaxy instance (16.04) in multi-thread mode ( 8 x web handler

Re: [galaxy-dev] tabular file displayed without tabs

s > isn't the case. > > > > On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard <carlfeberh...@gmail.com> > wrote: > >> Ok - if it's not zebra striped and it's word wrapping, then it's somehow >> not displaying as tabular - you're correct. >> >&

Re: [galaxy-dev] Current history via the REST API (or blend4j)

, Carl Eberhard <carlfeberh...@gmail.com> wrote: > Yeah - I understand what you're trying to do now and you're right. In an > effort to make the API stateless I think we've introduced a gap in > functionality for a good, practical use case. > > I've been wanting to replace the hi

Re: [galaxy-dev] tabular file displayed without tabs

highlighted and there is not word-wrapping on the file. However the > file that has the type tabular and displayed as text is word-wrapped with > no lines highlighted. I suspect its not actually recognized as tabular or > is being overridden where. > > > On Thu, Nov 12, 2015 at 10:23

Re: [galaxy-dev] Current history via the REST API (or blend4j)

There's a way to get the current history data through a non-api url: /history/current_history_json ...but, I don't believe those are accessible through any of the bio/blend libraries. Failing the above, is there some way to get the history ID from the UI? You can click the information button

Re: [galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

https://github.com/galaxyproject/galaxy/pull/1972 Thanks for letting us know about this. Let me know if you spot any problems with that fix. On Tue, Mar 22, 2016 at 8:32 AM, Carl Eberhard <carlfeberh...@gmail.com> wrote: > Hey, Hans > > Looks like a problem with the way we're lo

Re: [galaxy-dev] Login reguried causing nested main page loading

Hi, Christian and Ryan Which versions of Galaxy are you using when this happens? Thanks, Carl On Mon, Jan 11, 2016 at 9:03 AM, Ryan G wrote: > I've seen this as well. I find that restarting galaxy fixes the problem > but I'd love to know the underlying cause. >

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? the complete message ignore previous

( dataset.get_size() ) > >else: > >dataset.peek = 'file MDA_zip does not exist' > >dataset.blurb = 'file MDA_zip purged from disk' > >def display_peek( self, dataset ): > >try: > >return dataset.peek > >

Re: [galaxy-dev] How does one run Javascript or HTML as a tool? the complete message ignore previous

Hi, Bob There are a number of ways to visualize data in Galaxy, so let's settle on some terminology first for the three major ways: * *display applications*: these are definitions of external websites that can fetch galaxy datasets and display them in their visualization applications. Examples

Re: [galaxy-dev] Need urgent help: ItemOwnershipException: History is not owned by user

I'm stumped: - I'm not sure how that url (" http://galaxy.man.poznan.pl/history/view_multipl/api/histories/85b413e771c184a9/contents;) could have been formed - Calling that link from a local galaxy results in 'No route for' when the error is an api authentication 403 Maybe it's

Re: [galaxy-dev] Get dataset/API ids for a dataset

: is there an id that remains common to multiple outputs produced from one tool? Thank you, -Asma On Wed, Aug 26, 2015 at 10:07 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hi, Asma Sorry for the confusion. You may want to have a look here: http://docs.makotemplates.org/en/latest/index.html

Re: [galaxy-dev] Get dataset/API ids for a dataset

alone? -Asma On Fri, Aug 21, 2015 at 11:41 AM, Carl Eberhard carlfeberh...@gmail.com wrote: As far as I know, it's best to write tool wrappers as if they were meant to be called outside of Galaxy. In other words, it would not be best to try and get Galaxy dataset ids within the tool code

Re: [galaxy-dev] Get dataset/API ids for a dataset

history. this way there will be no ambiguity as to which bams are being accessed for viz. Is this intermediate way of getting dataset ids possible? Thank you -Asma On Wed, Aug 19, 2015 at 4:27 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Hi, Asma If you're looking through datasets

Re: [galaxy-dev] new visualization tool for composite datatype?

, Anne. -- *From:* Carl Eberhard carlfeberh...@gmail.com *Sent:* 18 August 2015 18:59 *To:* Anne Claire Fouilloux *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] new visualization tool for composite datatype? Hi, Anne Can you be more

Re: [galaxy-dev] new visualization tool for composite datatype?

Hi, Anne Can you be more specific about how you'd like to visualize the files? It sounds like you've already got a tool that will build an html file which is the classic way to make visualizations with galaxy. Now you'd like to make it more interactive? Do you already have javascript or python

Re: [galaxy-dev] Possible bug on Create a collection of paired datasets

Hi, Ata Roudgar It is indeed a bug. Thank you very much for the excellent and *helpful* report! We now have a fix for this on the release_15.05 branch of the github repository: https://github.com/galaxyproject/galaxy/commit/13a40b3ef206f8662a49dfd06fbbc05b026f8c64 It should fix the issue but

Re: [galaxy-dev] User is not allowed to view history

! Cheers, ~Lina On Mon, Jul 13, 2015 at 11:24 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hi, Lina Apologies for the delay. A few questions, please: - What version is your Galaxy instance running? - What URL or operation is the user trying when they get that error? Is it just

Re: [galaxy-dev] filtering html tables in a history item

Hi, Mark This could be done - but not easily. Essentially (if I understand correctly) you'd want to have a tool that uses a non-conventional control (the html table and row checkboxes) to allow the user to remove selected rows. One of the challenges is: how to create a new (smaller) dataset and

Re: [galaxy-dev] Fwd: History panel error

Hi, Jose Our next cycle includes some updates to the resubmission/hda-serialization code that's mentioned in your stack trace. You can try two things: 1) You can wait for us to officially publish our next stable release (15.05) at the beginning of next month and then update your instance. 2) You

Re: [galaxy-dev] Visualization in anonymous mode ?

, Loraine Le 08/01/2015 16:50, Carl Eberhard a écrit : Hi, Loraine It isn't possible currently without modifying the code for your installation. If you'd like I can provide a patch file that can be applied which will allow the visualization button (and the link to phyloviz

Re: [galaxy-dev] Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

In short: Question: How can I save a static snapshot...? You can't yet. Question: If so, can I then ...recreate the pie chart? No, not yet. Overall, these are features that we definitely want and we are working towards them. Questions remain for me, if I understand your original questions,

Re: [galaxy-dev] small issue with the black frame around displayed history item

Hi, Hans. Sorry for the confusion on this. I've got a card to improve that feature here: https://trello.com/c/xWdgs01z I may remove it for visualizations as they're too variable in where/how they display. Thanks for the info. Carl On Tue, Dec 2, 2014 at 11:41 AM, Hans-Rudolf Hotz h...@fmi.ch