[galaxy-dev] Deprecation of Sample Tracking and External Services
Hello everyone, We are considering to deprecate the Sample Tracking feature in Galaxy 18.01. Please let us know if you are using it so we can discuss alternative options. Thanks, Sam ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] unipept visualization
Hey Matthias, I noticed that this visualization has already been added and should be working in release 17.05 and a d3_hierarchy file. Its documented at https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations/unipept . Example files are available here: https://github.com/unipept/unipept-visualizations/tree/master/examples/data Now here is the issue I noticed, once you upload one of these example files, you need to select the file in the history, click on the pencil icon and change the datatype to 'd3_hierarchy' before attempting to visualize it. You cannot select the correct datatype in the upload view. I will test this a little bit more and fix it if necessary for the next release. I hope this helps. Thanks again. On Mon, Aug 28, 2017 at 4:23 AM, Matthias Bernt wrote: > Hi Sam, > > thanks for the answer. So far I have not configured anything, I was hoping > that it works out of the box :). > > Could you point me to some documentation where the setup is explained? > > Best, > Matthias > > On 25.08.2017 19:05, Aysam Guerler wrote: > >> Hi Matthias, >> >> Have you added the visulization to Charts or the regular Galaxy >> visualization framework? If it is the latter please make sure that you >> correctly specified the datatype in your XML file. Your visualization >> should than appear in the drop-down list in the history. >> >> Thanks, >> Sam >> >> On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt > m.be...@ufz.de>> wrote: >> >> Dear list, >> >> I can not get the wonderful unipept visualization to work on our >> Galaxy instance (a test instance on the dev branch). I get the >> message: >> "Unfortunately we could not identify a suitable plugin" >> >> The file I try to visualize was generated by unipept (pept2lca) and >> is of format d3_hierarchy. >> >> Could someone tell me if I need to install / configure something to >> get this running? >> >> Thanks a lot. >> >> Best, >> Matthias >> >> >> P.S. This might be also of interest for others, since this >> visualization is used in the Metaproteomics tutorial of the GTN. >> >> >> -- >> --- >> Matthias Bernt >> Bioinformatics Service >> Molekulare Systembiologie (MOLSYB) >> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ >> Helmholtz Centre for Environmental Research GmbH - UFZ >> Permoserstraße 15, 04318 Leipzig, Germany >> Phone +49 341 235 482296 , >> m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de >> > >> >> Sitz der Gesellschaft/Registered Office: Leipzig >> Registergericht/Registration Office: Amtsgericht Leipzig >> Handelsregister Nr./Trade Register Nr.: B 4703 >> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: >> MinDirig Wilfried Kraus >> Wissenschaftlicher Geschäftsführer/Scientific Managing Director: >> Prof. Dr. Dr. h.c. Georg Teutsch >> Administrative Geschäftsführerin/ Administrative Managing Director: >> Prof. Dr. Heike Graßmann >> --- >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ <http://galaxyproject.org/search/> >> >> >> > -- > > --- > Matthias Bernt > Bioinformatics Service > Molekulare Systembiologie (MOLSYB) > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > Helmholtz Centre for Environmental Research GmbH - UFZ > Permoserstraße 15, 04318 Leipzig, Germany > Phone +49 341 235 482296, > m.be...@ufz.de, www.ufz.de > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig > Wilfried Kraus > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Dr. h.c. Georg Teutsch > Administrative Geschäftsführerin/ Administrative Managing Director: > Prof. Dr. Heike Graßmann > --- > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] unipept visualization
Hi Matthias, Have you added the visulization to Charts or the regular Galaxy visualization framework? If it is the latter please make sure that you correctly specified the datatype in your XML file. Your visualization should than appear in the drop-down list in the history. Thanks, Sam On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt wrote: > Dear list, > > I can not get the wonderful unipept visualization to work on our Galaxy > instance (a test instance on the dev branch). I get the message: > "Unfortunately we could not identify a suitable plugin" > > The file I try to visualize was generated by unipept (pept2lca) and is of > format d3_hierarchy. > > Could someone tell me if I need to install / configure something to get > this running? > > Thanks a lot. > > Best, > Matthias > > > P.S. This might be also of interest for others, since this visualization > is used in the Metaproteomics tutorial of the GTN. > > > -- > > --- > Matthias Bernt > Bioinformatics Service > Molekulare Systembiologie (MOLSYB) > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > Helmholtz Centre for Environmental Research GmbH - UFZ > Permoserstraße 15, 04318 Leipzig, Germany > Phone +49 341 235 482296, > m.be...@ufz.de, www.ufz.de > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig > Wilfried Kraus > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Dr. h.c. Georg Teutsch > Administrative Geschäftsführerin/ Administrative Managing Director: > Prof. Dr. Heike Graßmann > --- > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Firefox drag and drop not working
Thanks for reporting this. A PR which should fix this issue is available here: https://github.com/galaxyproject/galaxy/pull/4496 On Fri, Aug 25, 2017 at 7:43 AM, SAPET, Frederic < frederic.sa...@biogemma.com> wrote: > Hi > > Same behavior for me. > Chrome (60.0) and IE (11.0.9600) are fine. > > Fred > > -Message d'origine- > De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la > part de Jochen Bick > Envoyé : vendredi 25 août 2017 10:39 > À : galaxy-dev@lists.galaxyproject.org > Objet : [galaxy-dev] Firefox drag and drop not working > > Hi all, > > we recently updated to our galaxy server and now we would like to use the > new feature drag and drop items from the history. It does not work with > Firefox but with chrome. In Firefox it says: > The address isn’t valid > > The URL is not valid and cannot be loaded. > > Web addresses are usually written like http://www.example.com/ > Make sure that you’re using forward slashes (i.e. /). > > Is there anything to enable, install, or set inside Firefox? > > Cheers Jochen > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] User Preferences not rendering view, insetting galaxy UI
Fyi. This has been resolved. The issue was related to server rewrite settings. A remaining question is if external users are able to change individual user settings. On Mon, Aug 21, 2017 at 7:31 PM, evan clark wrote: > I have been testing our new galaxy instance and came across an odd issue. > When a user is logged in and attempts to set their preferences the view > does not render and the galaxy UI is inset in the center section. This also > occurs when clicking public name. No errors are shown in the log. See image > in link > > https://www.dropbox.com/s/769f3nmot113205/Screen%20Shot%2020 > 17-08-21%20at%207.29.16%20PM.png?dl=0 > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] User Preferences not rendering view, insetting galaxy UI
Thanks for reporting this. Have you tried to refresh the browser? On Mon, Aug 21, 2017 at 7:31 PM, evan clark wrote: > I have been testing our new galaxy instance and came across an odd issue. > When a user is logged in and attempts to set their preferences the view > does not render and the galaxy UI is inset in the center section. This also > occurs when clicking public name. No errors are shown in the log. See image > in link > > https://www.dropbox.com/s/769f3nmot113205/Screen%20Shot%2020 > 17-08-21%20at%207.29.16%20PM.png?dl=0 > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Venn diagram example data
Sorry for the late response. So the venn diagram visualizes the overlap between sets. Each set is represented by entries in a column e.g. #SET1 SET2 SET3 A GA B HB C AG D BH E CX F DZ I hope this helps. Thanks Sam On Thu, Jul 27, 2017 at 11:33 AM, Peter Cock wrote: > Hi Steven, > > Just in case, you're not talking about my older simpler Galaxy Tool > for drawing simple Venn Diagrams, are you? > > https://toolshed.g2.bx.psu.edu/view/peterjc/venn_list > https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list > > This reminds me that I ought to update that tool to work with > dependencies via conda... > > Peter > > On Mon, Jul 24, 2017 at 2:16 PM, Steven Shen > wrote: > > Dear Galaxy list, > > > > I am interested in Galaxy Charts visualization.But venn diagram confuses > me > > when I upload my tabular data, it seems venn diagram need one column > > observations at least, actually I don't clear what should be contained in > > the one column observations. > > > > So is there any venn diagram example data or usage for this charts > plugin ? > > Sad to say I am not good at JavaScript :) > > > > Thank you very much. > > > > Regards, > > Steven > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/ > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] How to install Charts in command line ?
I agree, it should be straightforward. I will look into it. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] How to install Charts in command line ?
Hey, There is no documentation for this but it is possible. You need to install R and two R libraries (getopt, Matrix) in order to execute the charts R-script. Once R is configured you can add the charts tool to the tools directory and update your config/tool_conf.xml file accordingly before restarting your local instance. Having said this, can you specify in more detail why the tool installation fails. Can you install other tools from the toolshed without problems? I hope this helps. Thanks, Sam On Mon, Jul 17, 2017 at 9:53 AM, Steven Shen wrote: > Hi all， > > Cytoscape, Bar diagram(NVD3), Horizontal(NVD3) , and other NVD3 > visualization tools are working good on my local galaxy except the > jqplots, such as Box plot, Discrete Histogram, with error "This > visualization requires the 'charts' tool. Please make sure it is > installed." It seems i need to install Charts first. > > Actually Charts could be installed from the Tool Shed through the Admin > Interface, but it failed sometimes as the bad network. so is there any doc > about installing Charts/tools through command line? > > Thank you. > Steven > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] problem with column options
Hi Fabien, Are you referring to the entries shown in the drop-down when you click on the select field? Can you send a screenshot? Thank you, Sam On Thu, Jul 13, 2017 at 5:50 AM, fabien gogé wrote: > Dear All, > > I try to column options for a param linked to a dataset contained in my > history. > The first column of my dataset contains sample names. I want it propose me > all sample names contained in my dataset. It work when the dataset has few > columns but it doesn't work when my dataset has a lot of columns.Someone > has a solution? > > > > > > > > > Thank you for help, > -- > > Fabien Gogé > > UMR ITAP Irstea - SupAgro > Information – Technologies – Analyse environnementale – Procédés agricoles > Research Group ITAP Irstea - SupAgro > Information – Technologies – environmental Analysis – agricultural > Processes > > Irstea > BP 5095 ; 34196 MONTPELLIER Cedex 1 ; FRANCE > Tel: +33 (0)4 67 16 65 02 > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.
Hey, We are trying to resolve the issue so that others do not have to change the Apache settings. Is it possible to test this potential fix here: https://github.com/galaxyproject/galaxy/pull/4225 and comment on the issue? Thanks in advance, Sam On Thu, Jun 15, 2017 at 5:13 PM, Nicola Soranzo wrote: > According to the same documentation, you need it only if using the > mod_proxy Apache module with HTTP transport, but I'm using nginx, not > Apache, so I'm not the best person to ask. > > Cheers, > Nicola > > > On 15/06/17 15:55, Fernandez Edgar wrote: > > Thanks Nicola for the comfirmation. > > > > Would you mind explaining a little more: > > > > ProxyPass / http://127.0.0.1:8080/ > > Should I add this too? > > > > *Edgar Fernandez* > > System Administrator (Linux) > > Technologies de l'Information > > *Université de Montréal* > > > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 <(514)%20343-6111> poste 16568* > > > > *From:* Nicola Soranzo [mailto:nicola.sora...@gmail.com > ] *On Behalf Of *Nicola Soranzo > *Sent:* June 15, 2017 10:44 AM > *To:* SAPET, Frederic > ; Fernandez Edgar > ; > galaxy-...@bx.psu.edu > *Subject:* Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught > error. > > > > Hi Edgar, Frederic, > if you are using Apache as proxy for your Galaxy server, then you should > probably add > > AllowEncodedSlashes NoDecode > > > to your Apache config, see https://galaxyproject.org/ > admin/config/apache-proxy/#allow-encoded-slashes-in-urls > > Cheers, > Nicola > > On 15/06/17 15:35, SAPET, Frederic wrote: > > Hi > > > > Same for me. > > But It looks like to be related with tools installed via the toolshed (Ie > : bedtools, emboss, blast+ suite…). > > My own tools seem to be ok. > > > > Just like you Edgar, nothing in the log… > > > > Fred > > > > *De :* galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org > ] *De la part de* Fernandez > Edgar > *Envoyé :* mercredi 14 juin 2017 17:11 > *À :* galaxy-...@bx.psu.edu > *Objet :* [galaxy-dev] new installation galaxy-17.05 - Uncaught error. > > > > Hey Guys, > > > > Hope everyone is doing ok. > > > > I have a small issue with a brand new installation of galaxy-1705. > > It starts properly and I installed some tools. > > But when I try to test any tools I get and “Uncaught error” (see picture). > > > > I can’t find anywhere in the logs what is happening. > > > > Any ideas? > > > > Regards, > > > > *Edgar Fernandez* > > System Administrator (Linux) > > Technologies de l'Information > > *Université de Montréal* > > > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 <(514)%20343-6111> poste 16568* > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/ > > > > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] cytoscape & charts
Hi Matthias, Can you verify that the file is recognized as 'sif'-file in the Galaxy history and not as 'txt'-file? Please change the format if necessary. I hope this helps, Sam On Wed, Apr 5, 2017 at 7:01 AM, Matthias Bernt wrote: > Dear galaxy-dev, > > I just wanted to test the exciting cytoscape charts plugin that was just > announced: https://github.com/galaxyproject/galaxy/pull/3817 > > So I created a small sif file > > nodeA xx nodeB > nodeB xx nodeC > nodeC xx nodeD > nodeD xx nodeA > nodeB xx nodeD > > I guess I have to click the "Visualize" button of the data set where I > have the options "Charts" and "Graph Visualizations". The former has only > oine option: Multiple Sequence Alignment (BioJS). So I guess its the latter > which shows me a graph. But it looks different to the example in the pull > request, e.g. node names are not shown and I can not interact as shown in > the three figures. > > Is there some docomentation that I could read. In general I would be > interested to read about the Charts. > > Would be grateful about some pointers. > > Cheers, > Matthias > > > > -- > > --- > Matthias Bernt > Bioinformatics Service > Molekulare Systembiologie (MOLSYB) > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > Helmholtz Centre for Environmental Research GmbH - UFZ > Permoserstraße 15, 04318 Leipzig, Germany > Phone +49 341 235 482296, > m.be...@ufz.de, www.ufz.de > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig > Wilfried Kraus > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Dr. h.c. Georg Teutsch > Administrative Geschäftsführerin/ Administrative Managing Director: > Prof. Dr. Heike Graßmann > --- > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] multiple datatypes input in 16.07
Hi Chris, I am glad that we figured this out. So I am not sure what the best strategy for datatypes with code dependencies is, we should open a new thread or git issue and see if someone can help with that. Thanks, Sam On Wed, Dec 14, 2016 at 10:59 AM, Cristel Thomas wrote: > Hi again, > ok, ran some more tests - we switched to a new dev server recently and we > were having the issue because of the R/rpy2 thing. > > With that taken care of though, we still have files in the dropdown that > shouldn't be there - no more FCS, but .ypnb still show up. I guess this is > because 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 > wrote: > >> 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 script, it requires flowCore installed in R). >> We have R installed on our instance and still have the issues I described >> earlier (though I will double check tomorrow and keep you posted). >> >> In the long run the rpy2 thing might be an issue. We want to add our >> tools and the datatypes to galaxy. I'm not sure how to get around to doing >> it without rpy2. I'd like to keep a sniffer function in there. >> >> Thanks again, >> Cris >> >> On Tue, Dec 13, 2016 at 1:24 PM, Aysam Guerler >> wrote: >> >>> Hey Cris, >>> >>> Dannon and I figured out, that the problem is that your datatypes are >>> not loaded properly, due to these two invalid imports: >>> >>> https://github.com/ImmPortDB/immport-galaxy/blob/release_16. >>> 07/lib/galaxy/datatypes/flow.py#L13 >>> >>> Removing them fixes the issue. The error for this is shown in the server >>> log. >>> >>> Thanks, >>> Sam >>> >> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple datatypes input in 16.07
Hey Cris, Dannon and I figured out, that the problem is that your datatypes are not loaded properly, due to these two invalid imports: https://github.com/ImmPortDB/immport-galaxy/blob/release_16.07/lib/galaxy/datatypes/flow.py#L13 Removing them fixes the issue. The error for this is shown in the server log. Thanks, Sam ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple datatypes input in 16.07
Ok, let me look a little bit further then. Can you send me the corresponding tool xml file and let me know which datatypes appear in the dropdown list and which of those you would not expect to see? Ideally we can reproduce it with datatypes available to everyone, so I can test it locally. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple datatypes input in 16.07
Ok, so this seems to work properly, and implicit conversion is the reason why you see html and text, but not png and pdf files. Currently there is no option to disable implicit conversion but its an enhancement we can suggest to be implemented by creating a github issue. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple datatypes input in 16.07
Thanks for the quick response. What is the set of datatypes you are specifying? It is possible that one of the specified datatypes can be implicitly converted to html and text e.g. a fasta file will be listed even if only tabular has been specifed as valid datatype. In other 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 wrote: > Hi Sam, > I'm not sure what tools have multiple datatypes as input on usegalaxy.org > (and my files are still waiting to be uploaded for some reasons.) > I can give you more details though. Those are tools we developed for flow > cytometry with new datatypes. I wonder if the issue is with the fact that > we added datatypes and I didn't do it right, although again, we don't have > any issues running 16.01 with those datatypes. > What I found so far on our test instance is the following: > - the problem exists with all tools on the instance, not just the few that > are set to take in several datatypes. > - the files that appear in the selection drop-down are of several > datatypes. I thought it was limited to the new datatypes we have defined, > but .html, .ypnb and text files are picked up although interestingly .png > and .pdf don't show up. > - the problem disappears when I limit the datatypes back to one for the 3 > tools that we had set as accepting several datatypes. > thanks for your help! > -Cris > > On Mon, Dec 5, 2016 at 10:29 AM, Aysam Guerler > wrote: > >> Hey Cris, >> >> Thanks for reporting this. I am looking into it. In the meanwhile, I am >> wondering if 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 >> wrote: >> >>> 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 what's going on? >>> >>> Thanks much, >>> Cris >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple datatypes input in 16.07
Hey Cris, Thanks for reporting this. I am looking into it. In the meanwhile, I am wondering if 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 wrote: > 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 what's going on? > > Thanks much, > Cris > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Code File Execution
Hey Katherine, It happens in basic.py. The code tag is executed to generate select options there. Look at: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parameters/basic.py#L778 Bye, Sam On Mon, Nov 21, 2016 at 1:46 PM, Peter Cock wrote: > Are you asking how Galaxy takes the user-entered parameters > (requested in the tool XML file with tags) and builds a > command line string using the Cheetah-format template defined > in the tag? > > At least part of the answer to that is the ToolEvaluator object: > > https://github.com/galaxyproject/galaxy/blob/ > 71cea6604d43c5fe6215f5656462ba6c1af69bb6/lib/galaxy/tools/ > evaluation.py#L454 > > Peter > > On Mon, Nov 21, 2016 at 6:37 PM, Katherine Beaulieu > wrote: > > Hi Everyone, > > Does anyone know how execution of code files happens? Is there a function > > somewhere that fills the parameters in? > > Cheers, > > Katherine > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: Workflow Execution Files
Hey Katherine, Do you attach the values to a valid step? If so I have to look more into it in order to figure out why the values do not make it through. Thanks, Sam On Mon, Oct 24, 2016 at 2:55 PM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > > -- Forwarded message -- > From: Katherine Beaulieu > Date: Mon, Oct 24, 2016 at 2:55 PM > Subject: Re: [galaxy-dev] Workflow Execution Files > To: Aysam Guerler > > > Awesome thanks Aysam! I was wondering if you know what happens to the job > parameters once they go through 'POST'? I am trying to add my own parameter > which should show up in the database. I was successful for an individual > job in tool-form.js, by just adding an attribute to the job_def.inputs > parameter but in tool-form-composite.js, just adding a parameter to > job_def.parameters[step size][job_input_id] doesn't automatically add to > the database. > Thanks for the help! > > On Mon, Oct 24, 2016 at 9:57 AM, Aysam Guerler > wrote: > >> Hi Katherine, >> >> The tool form is build and submitted to the API through >> tool-form-composite.js. >> >> Sam >> >> On Mon, Oct 24, 2016 at 9:29 AM, Katherine Beaulieu < >> katherine.beaulieu...@gmail.com> wrote: >> >>> Hi Everyone, >>> Does anyone know what files workflow execution goes through? I had >>> assumed it just went through the same files as individual jobs for each >>> step but I don't think that's the case. I was looking at tool-form.js but >>> it doesn't seem to be executing that file. >>> Thanks! >>> Katherine >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow Execution Files
Hi Katherine, The tool form is build and submitted to the API through tool-form-composite.js. Sam On Mon, Oct 24, 2016 at 9:29 AM, Katherine Beaulieu < katherine.beaulieu...@gmail.com> wrote: > Hi Everyone, > Does anyone know what files workflow execution goes through? I had assumed > it just went through the same files as individual jobs for each step but I > don't think that's the case. I was looking at tool-form.js but it doesn't > seem to be executing that file. > Thanks! > Katherine > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] workflow problems
I remember this issue and that it was fixed. Updating to a newer revision should resolve it. 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, >> 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 to the name >> and then 'run', or by clicking on run from the workflow editor, it takes me >> to the interactive tour page. >> >> Anyone else? >> >> Thanks, >> Cris >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy.masthead.js change
Hi Mohamed, the masthead file has been moved to https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/layout/masthead.js . On Tue, May 17, 2016 at 4:12 AM, Mohamed Kassam wrote: > Dear all, > I would like to know which file replaced the galaxy.masthead.js file. > Because I was putting in the banner the name and the logo of our local > galaxy. > > Best regards, > > > Mohamed > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Downgrade tool upload tool
Thanks Peter. I think you are right and that its a change in Galaxy which causes this routing issue. I have prepared a fix for it: https://github.com/galaxyproject/galaxy/compare/dev...guerler:fix_upload_link_000?expand=1. Ill double check tomorrow with those working on the routing and then issue a PR. Thanks a lot for reporting this Makis. On Mon, Feb 29, 2016 at 8:17 AM, Peter Cock wrote: > Thanks for clarifying Makis, > > I think this change is likely due to changes in Galaxy rather than > in the upload tool itself. On our (slightly out of date) Galaxy or the > public server, that URL no longer loads the original tool form - > you get the new drag-and-drop upload interface. > > I would guess some of the special case code like this matters: > > https://github.com/galaxyproject/galaxy/blob/fe6d22e1a7e4e6d38b15f4128554783765bc69a1/client/galaxy/scripts/mvc/tool/tools.js#L525 > > Probably Sam (Aysam) can give you more practical advice (CC'd)? > > Peter > > On Mon, Feb 29, 2016 at 12:29 PM, Makis Ladoukakis > wrote: > > I am making some clickable buttons in the home page of my instance > through a > > java script that is called from the welcome.html file. These buttons > > correspond to my most used tools. For example I have a section like this: > > > > > > > > > > > > > > > src="feimg/GetData.gif"/> > > > > > href="http://myserver/galaxy/tool_runner?tool_id=upload1"; > > target="_parent"> > height=300%/> > > > href="http://myserver/galaxy/library/browse_libraries"; > target="_parent"> > src="feimg/Libraries.gif" width=250% height=300%/> > > > > > > > > > > > > > > indicating two buttons one for the upload tool and one for the libraries. > > The libraries button work but when I click on the button for the upload > tool > > the webpage just refreshes instead of opening the tool. This worked > > perfectly with the previous version of the upload tool and I was thinking > > how to get it back. > > > > Thank you, > > Makis > > > > > >> Date: Mon, 29 Feb 2016 11:39:26 + > >> Subject: Re: [galaxy-dev] Downgrade tool upload tool > >> From: p.j.a.c...@googlemail.com > >> To: makis4e...@hotmail.com > >> CC: j...@galaxyproject.org; galaxy-...@lists.bx.psu.edu; > >> galaxy-dev@lists.galaxyproject.org > > > >> > >> Hi Makis, > >> > >> The upload tool is a little special in that it is used internally by > >> Galaxy and doesn't entirely behave like a normal tool. > >> > >> What are you trying to achieve by "downgrading" it? > >> > >> Peter > >> > >> On Mon, Feb 29, 2016 at 11:29 AM, Makis Ladoukakis > >> wrote: > >> > What about if I used a second "tool upload" tool? I took the python > >> > script > >> > from an earlier version and named it upload_old.py and did the same > for > >> > the > >> > xml file (upload.xml -> upload_old.xml) while changing the latter to > >> > call > >> > the new python script. Nevertheless when I did that and tried to run > it > >> > I > >> > got a popup window with the following error: > >> > > >> > Tool request failed > >> > > >> > Uncaught exception in exposed API method: > >> > > >> > > >> > Is there a way to make this work? Or maybe another workaround? > >> > > >> > Thank you in advance, > >> > Makis > >> > > >> > > >> > > >> > > >> > From: j...@galaxyproject.org > >> > Date: Fri, 26 Feb 2016 10:22:44 -0800 > >> > Subject: Re: [galaxy-dev] Downgrade tool upload tool > >> > To: makis4e...@hotmail.com > >> > CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org > >> > > >> > > >> > Hello, > >> > > >> > The Upload tool is a direct component of Galaxy. To use an earlier > >> > version > >> > of the tool, I believe that you would have to run an earlier version > of > >> > Galaxy. > >> > > >> > Others here can amend this, if they know of an alternative. > >> > > >> > Thanks, > >> > > >> > Jen > >> > > >> > -- > >> > Jennifer Hillman-Jackson > >> > Galaxy Application Support > >> > http://usegalaxy.org > >> > http://galaxyproject.org > >> > http://biostar.usegalaxy.org > >> > > >> > > >> > On Fri, Feb 26, 2016 at 4:01 AM, Makis Ladoukakis > >> > > >> > wrote: > >> > > >> > Hello everyone, > >> > > >> > I was wondering whether it's possible to downgrade the upload tool to > >> > the > >> > previous version(1.1.4). > >> > > >> > I copied the upload.py and upload.xml scripts from a previous galaxy > >> > version > >> > to the tools/data_source/ directory and reloaded the tool as admin but > >> > it > >> > hasn't changed even when I restarted the server. > >> > > >> > Do I have to change something else in addition? > >> > > >> > Thank you, > >> > Makis > >> > > >> > ___ > >> > Please keep all replies on the list by using "reply all" > >> > in your mail client. To manage your subscriptions to this > >> > and other Galaxy li
Re: [galaxy-dev] Filtering dynamic options in tool with tagset
No worries. Although it is 'deprecated' it will be not be removed until we have a good alternative. On Wed, Jan 27, 2016 at 4:36 AM, Matthias De Smet wrote: > So it seems it has been deprecated a bit prematurely. Maybe the Galaxy > team should “undeprecate” it untill a viable alternative is found. > > Anyway, thanks again! > > Matthias > > > Op 27 jan. 2016, om 10:33 heeft Hans-Rudolf Hotz het > volgende geschreven: > > > > > > > > On 01/27/2016 10:29 AM, Matthias De Smet wrote: > >> Hi Hans-Rudolf > >> > >> Thanks again, you’re a lifesaver! > >> Any suggestions on how I could eliminate the tag, as the wiki > states it’s deprecated? > > > > well, it has been 'deprecated' for many years now. > > > > > >> I checked out but don’t see a straightforward wau to get the > same results. > > > > same for me :( > > > > > > Hans-Rudolf > > > > > > > > > >> > >> Matthias > >> > >>> Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz het > volgende geschreven: > >>> > >>> Hi Matthias > >>> > >>> I don't think you can do that...I would delegate the filtering to the > 'list_files' function, i.e. by calling: > >>> > >>> list_files(archive_source,query) > >>> > >>> > >>> Regards, Hans-Rudolf > >>> > >>> > >>> On 01/27/2016 10:07 AM, Matthias De Smet wrote: > > Hi All, > > I’m trying to implement a tool that get a list of options through the > “dynamic_options” tag. I try to filter the options that get returned with > another param, but it doensn’t seem to work. > > my tool xml looks like this > > > from the archive to a data library > > > test.sh > $log > > > label="Choose source archive"> > > > > > > > > > > > > > > > > > > > > > > > Anyone with experience implementing filters? (Gx 15.10 on Ubuntu > 14.04.3) > > Thanks! > Matthias > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > >> > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool data_column param issue under workflow mode
Thx for reporting this. I am looking into it. On Wed, Nov 25, 2015 at 4:53 AM, Nils Paulhe wrote: > Hi! > > Same problem here but only if my workflow start with an "input type" tool > or any other tool, i can not select an option in list for workflow's other > tools > cf: > https://dl.dropboxusercontent.com/u/86878089/Screen%20Shot%202015-11-25%20at%2010.37.26.png > > definitely not a data type problem ^^' > > sincerely > > nils > > On 25 November 2015 at 10:30, Christian Brenninkmeijer < > christian.brenninkmei...@manchester.ac.uk> wrote: > >> Hi >> >> If you load a tabular table with type auto there is a possibility that it >> incorrectly sniffed as a csv file. With type csv the columns are split on >> commas and not tabs so the data appears in one column. >> >> This is especially the case for tab separated files that do not have row >> names and therefore the same number of tabs in the header row as the next >> row. >> >> Manually change the type to tabular which will solve the problem. >> >> One possible solution which add a stricter csv sniff method is in: >> >> https://github.com/galaxyproject/galaxy/pull/1156 >> >> regards >> Christian >> University of Manchester >> -- >> *From:* Christian Brenninkmeijer >> *Sent:* Wednesday, November 25, 2015 9:23 AM >> *To:* FGiacomoni INRA >> *Subject:* RE: [galaxy-dev] tool data_column param issue under workflow >> mode >> >> Hi >> >> If you load a tabular table with type auto there is a possibility that it >> incorrectly sniffed as a csv file. With type csv the columns are split on >> commas and not tabs. >> >> This is especially the case for tab separated files that do not have row >> names and therefor the same number of tabs in the header row as the next >> row. >> >> Manually change the type to tabular which will solve the problem. >> >> One possible solution which add a stricter csv sniff is in: >> >> https://github.com/galaxyproject/galaxy/pull/1156 >> >> regards >> Christian >> -- >> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on >> behalf of FGiacomoni INRA [franck.giacom...@clermont.inra.fr] >> *Sent:* Tuesday, November 24, 2015 2:16 PM >> *To:* galaxy-dev@lists.galaxyproject.org >> *Subject:* [galaxy-dev] tool data_column param issue under workflow mode >> >> Dears, >> We observed this issue under galaxy release 15.07. >> Tools with a param tag and type="data_column" in their xml file are >> impossible to set on a workflow "run" mode. >> The value of the column stay at "column 1" or void even if your tabular >> file has more than one column. >> >> The setting of the tool is ok in the "analyze data" mode : you can change >> the value of the column. >> >> We tested this issue with home made tools but also with Merge Columns >> (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. >> and we detected the issue on the galaxy main instance too... >> >> Any idea ? >> Thanks >> Marion & Franck >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Question about using dynamic options and refresh_on_change for rendering 2 associated select lists
Well I guess it doesn't matter, glad it works now. On Wed, Sep 30, 2015 at 2:47 PM, Aysam Guerler wrote: > If the select field did not properly render before, it should not render > properly now. > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Question about using dynamic options and refresh_on_change for rendering 2 associated select lists
If the select field did not properly render before, it should not render properly now. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Question about using dynamic options and refresh_on_change for rendering 2 associated select lists
Hi Greg,
I am not sure which data source would be the most suitable for your use
case (maybe someone else can help here) but either should work and refresh
properly if filtered properly.
Thanks,
Sam
On Fri, Sep 18, 2015 at 11:02 AM, Greg Von Kuster wrote:
> Hi Sam,
>
> I have another related question that I’m hoping you can help with. In my
> case, the dataset contains the information I need as the contents of the
> test_select_options.txt file, so that file is not static. The values that
> are needed to provide the options in my select list 2 would have to come
> from the metadata generated for the dataset. I investigted using the
> dynamic otions “from_file” approach, but looking at the current tools that
> use that approach (e.g., maf tools), it seems like it is not quite geared
> toward what I need.
>
> Thans again!
>
> Greg
>
>
>
> On Sep 18, 2015, at 10:41 AM, Greg Von Kuster wrote:
>
> Hi Sam,
>
> Thanks for the pointer to the Trello card. I noticed the card is kind of
> old (I think it predates data tables), so I just wanted to confirm the
> approach. For my tool, should I use the existing from_file option for
> dynamic options (call the file test_select_options.txt”) with the file
> located in a tool-data directory within a TS repo? The current TS install
> process would then install test_select_options.txt into the
> ~/shed_tool_data directory within the Galaxy root. Is this still the
> advised approach, or should the tool that requries test_select_options.txt
> be of type “manage_data”?
>
> Thanks!
>
> Greg
>
>
> On Sep 18, 2015, at 9:42 AM, Aysam Guerler
> wrote:
>
> Hi Greg,
>
> The tool form supports multiple dynamic fields which depend on each other.
> You may want to take a look at this:
> https://trello.com/c/NOmjJxCi/428-305-potential-bug-in-dynamic-options-filters
> .
>
> Hope this helps,
> Sam
>
> On Fri, Sep 18, 2015 at 8:30 AM, Greg Von Kuster wrote:
>
>> Hello all,
>>
>> I’m working on adding support to the Galaxy framework for datatypes in
>> the constructive solid geometry (CSG) space and I have several working
>> Galaxy tools and a visualization plugin that deal with 3d shapes in this
>> environment. All of this work will soon be contributed to open source.
>>
>> For one of the tools, I need to provide 2 select lists on the tool form
>> that are associated in such a way that when an option in select list 1 is
>> chosen, the options in select list 2 are altered and re-rendered. This
>> behavior would probably use a combination of dynamic options and
>> refresh_on_change between the 2 associated select lists.
>>
>> I’ve not seen a tool that does this precisely, so I’m hoping that if it
>> is currently possible to do this within Galaxy tools, someone will point me
>> to an example.
>>
>> If it is not currently possible, I will contribute a PR for supporting
>> it, but would like some input as to how it should be done.
>>
>> Dynamic options are currently rendered using 4 approaches; from_file,
>> from_dataset, from_parameter and from_data_table. One or more of several
>> filters can then be applied to the options to alter them if desired.
>>
>> Since these CSG tools involve new datatypes, I have flexibility into how
>> the metadata elements are set up that are needed to render these 2 select
>> lists. A dictionary may work where the metadata element contents look like
>> this:
>>
>> {a: [‘1’, ‘2’], b: [‘3’, ‘4’] }
>>
>> The options in select list 1 would be ‘a’ and ‘b’. When ‘a’ is selected,
>> select list 2 would have options ‘1’ and ‘2’, and when ‘b’ is selected,
>> select list 2 would have options ‘3’ and ‘4’.
>>
>> To support this approach, perhaps dynamic options could be enhanced to
>> include a from_dict option. There would be some complxity involved in
>> associating the lists using refresh_on_change so that select list 2 is
>> refreshed with the correct options when select list one is changed. I
>> haven’t yet worked out these details.
>>
>> Also, using a dictionary will not keep order for the options, so perhaps
>> a list of tuples would be better?
>>
>> [ [ ‘a’, [‘1’, ‘2’]], [‘b’, [‘3’, ‘4’]]]
>>
>> Can someone let me know if this is currently possible, and if so, an
>> example tool that does it? If it’s not possible, does the above approach
>> seem reasonable, or is there a better way?
>>
>> Thanks very much,
>>
>> Greg Von Kuster
>>
>> ___
>> Please keep all replies on the list by using "reply all"
Re: [galaxy-dev] Question about using dynamic options and refresh_on_change for rendering 2 associated select lists
Hi Greg,
The tool form supports multiple dynamic fields which depend on each other.
You may want to take a look at this:
https://trello.com/c/NOmjJxCi/428-305-potential-bug-in-dynamic-options-filters
.
Hope this helps,
Sam
On Fri, Sep 18, 2015 at 8:30 AM, Greg Von Kuster wrote:
> Hello all,
>
> I’m working on adding support to the Galaxy framework for datatypes in the
> constructive solid geometry (CSG) space and I have several working Galaxy
> tools and a visualization plugin that deal with 3d shapes in this
> environment. All of this work will soon be contributed to open source.
>
> For one of the tools, I need to provide 2 select lists on the tool form
> that are associated in such a way that when an option in select list 1 is
> chosen, the options in select list 2 are altered and re-rendered. This
> behavior would probably use a combination of dynamic options and
> refresh_on_change between the 2 associated select lists.
>
> I’ve not seen a tool that does this precisely, so I’m hoping that if it is
> currently possible to do this within Galaxy tools, someone will point me to
> an example.
>
> If it is not currently possible, I will contribute a PR for supporting it,
> but would like some input as to how it should be done.
>
> Dynamic options are currently rendered using 4 approaches; from_file,
> from_dataset, from_parameter and from_data_table. One or more of several
> filters can then be applied to the options to alter them if desired.
>
> Since these CSG tools involve new datatypes, I have flexibility into how
> the metadata elements are set up that are needed to render these 2 select
> lists. A dictionary may work where the metadata element contents look like
> this:
>
> {a: [‘1’, ‘2’], b: [‘3’, ‘4’] }
>
> The options in select list 1 would be ‘a’ and ‘b’. When ‘a’ is selected,
> select list 2 would have options ‘1’ and ‘2’, and when ‘b’ is selected,
> select list 2 would have options ‘3’ and ‘4’.
>
> To support this approach, perhaps dynamic options could be enhanced to
> include a from_dict option. There would be some complxity involved in
> associating the lists using refresh_on_change so that select list 2 is
> refreshed with the correct options when select list one is changed. I
> haven’t yet worked out these details.
>
> Also, using a dictionary will not keep order for the options, so perhaps a
> list of tuples would be better?
>
> [ [ ‘a’, [‘1’, ‘2’]], [‘b’, [‘3’, ‘4’]]]
>
> Can someone let me know if this is currently possible, and if so, an
> example tool that does it? If it’s not possible, does the above approach
> seem reasonable, or is there a better way?
>
> Thanks very much,
>
> Greg Von Kuster
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] dynamic_options within repeat or conditional block
Hey Linda, This seems to be an issue which has already been fixed. Could you please update your instance and/or let me know at which commit it is? Thank you, Aysam On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker wrote: > Hi All, > > I am relatively new to galaxy and recently had to take over the work on > several tools. > After the last galaxy update, one of them stopped working. > > Old working code: > > > refresh_on_change="true" >dynamic_options='filter_column2(library_file, col_type, > polarity)' /> > > > This worked perfectly, but now, the select shows me "no options available" > When i move the param-tag out of the repeat block, it works again. > Also, when i put this param within a conditional like: > > >label="Select column name preference?" /> > >refresh_on_change="true" > dynamic_options='filter_column2(library_file,col_type,polarity)'/> > > > > > > > the dynamic_options also does not work. > I found a trello -bug report: > https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-work-in-repeats > This seems to be my problem too. > > Can someone confirm for me that it is not possible to use the > dynamic_options from within a repeat or conditional block, or am i missing > something? Otherwise i have to come up with some sort of workaround. > > Thank you, > > Linda Bakker > > > -- > Linda Bakker > Bioinformatics Research Assistant > Plant Research International, Wageningen UR > Building 107 (Radix), room W1.Fa.054 > Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands > tel: +31-317-480756 > email: linda.bak...@wur.nl > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)
Hi Damion,
An initial implementation of the library dataset tool parameter (which
allows the selection of multiple library datasets) is currently in the
pipeline https://github.com/galaxyproject/galaxy/pull/132. After some
review the feature should be available in the default branch, however you
may try it now if you are interested.
Thanks,
Sam
On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion
wrote:
> I was successful getting library dataset selection and form submission to
> happen within tool form tool form input -
> Yay! But it appears one last fix (besides the "url:
> "/visualization/list_libraries",' bug) is needed to enable history tool
> item to be RERUN.
>
> So if a galaxy dev can tackle this, great! Otherwise I'll have to drop
> this approach :<(
>
> *
> For others who may need...
>
> tool form's param:
>
> label="Reference Bin file" help="Select one reference bin at a time from
> the popup window's Reference Bin library."/>
>
> tag contents
>
> #if $library_datasets
> -B "
> #for $i, $dataset in enumerate($library_datasets)
> #$dataset.get_file_name()
> $dataset.id
> #end for
> "
> #end if
>
> Successfully submits either the full file path of selected dataset, or its
> id.
>
> *
> However trying to rerun this history tool item gets us an error (not
> related to the above contents):
>
> Error Traceback:
> View as: Interactive | Text | XML (full)
> ⇝ AttributeError: 'int' object has no attribute 'id'
>
> Module galaxy.tools.parameters.basic:146 in value_to_basic
> view
> >> return self.to_string( value, app )
> Module galaxy.tools.parameters.basic:2406 in to_string
> app
> ldda331
> self object at 0x7fced01d2090>
> value [331]
> >> return [ldda.id for ldda in value]
> AttributeError: 'int' object has no attribute 'id'
>
> which is in /lib/galaxy/tools/parameters/basic.py:
>
> class LibraryDatasetToolParameter( ToolParameter ):
> """
> Parameter that lets users select a LDDA from a modal window,
> then use it within the wrapper.
> """
>
> ...
> def to_string( self, value, app ):
> if not value:
> return value
> return [ldda.id for ldda in value]
>
> "Value" is getting an array of dataset ids, whereas this method is
> expecting value to be a list of dataset objects. I tried changing ldda.id
> to just "id" but found other parts of LibraryDatasetTool code were broken
> as they too were expecting an object. Maybe this is related to the tool
> job's history detail link showing "Reference Bin file" as a string label of
> an object?:
>
> Input Parameter Value Note for rerun
> BLAST results as XML240: megablast Pasted Entry vs
> 16SMicrobial.fasta
> Reference Bin file
> []
> Tabular Report Column LabelsShort name
> HTML Report templatetemplates.html_report
>
>
>
>
> The other bug:
>
> 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy
> installs that have a prefix so that needs adjustment:
>
> $(".add-librarydataset").click(function() {
> var link = $(this);
> $.ajax({
> url: "/visualization/list_libraries",
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
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Re: [galaxy-dev] Multiple-select checkbox parameters not using default values
A fix for this is on the way. On Fri, Mar 27, 2015 at 10:53 AM, Peter Cock wrote: > Hi all, > > Unfortunately it appears that the new-look check box controls are wrongly > defaulting to ticking the first item rather than following the defaults > given. > > This is a recent regression which I noticed on updating our production > Galaxy > to the 15.03 release which included a number of visual style updates to the > parameter widgets: > > > https://trello.com/c/8alIlOUN/2590-param-type-select-display-checkboxes-multiple-true-default-values-not-used > > e.g. this example from the BLAST+ wrappers should default to all the > checkboxes being checked (ticked): > > display="checkboxes" label="Standard columns"> > qseqid = Query Seq-id (ID of > your sequence) > sseqid = Subject Seq-id (ID of > the database hit) > pident = Percentage of > identical matches > length = Alignment length > mismatch = Number of > mismatches > gapopen = Number of gap > openings > qstart = Start of alignment in > query > qend = End of alignment in > query > sstart = Start of alignment in > subject (database hit) > send = End of alignment in > subject (database hit) > evalue = Expectation value > (E-value) > bitscore = Bit score > > > Thus far I've only noticed this where multiple="true" since for single > select > parameters I've normally opted for the radio-select button instead. > > Does anyone use multiple="false" (default) with display="checkboxes"? > > Peter > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] charts
Hi Michael, We have update the repository. Please re-install the Charts plugin. It should work now. Thanks, Sam On Tue, Feb 24, 2015 at 9:39 AM, Michael Thon wrote: > Hi - > I tried to install the package charts but it failed on the dependency > charts_r_packages with this error: > > File > "/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 139, in install_and_build_package_via_fabric tool_dependency = > self.install_and_build_package( tool_shed_repository, tool_dependency, > actions_dict ) File > "/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", > line 97, in install_and_build_package initial_download=True ) File > "/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", > line 32, in execute_step initial_download=initial_download ) File > "/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 1238, in execute_step self.url_download( work_dir, filename, url, > extract=False ) File > "/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", > line 183, in url_download raise Exception( err_msg ) Error downloading from > URL http://cran.r-project.org/src/contrib/Matrix_1.1-4.tar.gz: HTTP Error > 404: Not FoundInstalled tool dependencies: charts_r_packages > > It looks like matrix is now at version: Matrix_1.1-5.tar.gz > > -Mike > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)
Hey Damion,
Thanks a lot for the description. We are currently switching the tool form
to a newer version but I will look into this fix soon and should be able
transfer it.
Thanks,
Sam
On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion
wrote:
> I was successful getting library dataset selection and form submission to
> happen within tool form tool form input -
> Yay! But it appears one last fix (besides the "url:
> "/visualization/list_libraries",' bug) is needed to enable history tool
> item to be RERUN.
>
> So if a galaxy dev can tackle this, great! Otherwise I'll have to drop
> this approach :<(
>
> *
> For others who may need...
>
> tool form's param:
>
> label="Reference Bin file" help="Select one reference bin at a time from
> the popup window's Reference Bin library."/>
>
> tag contents
>
> #if $library_datasets
> -B "
> #for $i, $dataset in enumerate($library_datasets)
> #$dataset.get_file_name()
> $dataset.id
> #end for
> "
> #end if
>
> Successfully submits either the full file path of selected dataset, or its
> id.
>
> *
> However trying to rerun this history tool item gets us an error (not
> related to the above contents):
>
> Error Traceback:
> View as: Interactive | Text | XML (full)
> ⇝ AttributeError: 'int' object has no attribute 'id'
>
> Module galaxy.tools.parameters.basic:146 in value_to_basic
> view
> >> return self.to_string( value, app )
> Module galaxy.tools.parameters.basic:2406 in to_string
> app
> ldda331
> self object at 0x7fced01d2090>
> value [331]
> >> return [ldda.id for ldda in value]
> AttributeError: 'int' object has no attribute 'id'
>
> which is in /lib/galaxy/tools/parameters/basic.py:
>
> class LibraryDatasetToolParameter( ToolParameter ):
> """
> Parameter that lets users select a LDDA from a modal window,
> then use it within the wrapper.
> """
>
> ...
> def to_string( self, value, app ):
> if not value:
> return value
> return [ldda.id for ldda in value]
>
> "Value" is getting an array of dataset ids, whereas this method is
> expecting value to be a list of dataset objects. I tried changing ldda.id
> to just "id" but found other parts of LibraryDatasetTool code were broken
> as they too were expecting an object. Maybe this is related to the tool
> job's history detail link showing "Reference Bin file" as a string label of
> an object?:
>
> Input Parameter Value Note for rerun
> BLAST results as XML240: megablast Pasted Entry vs
> 16SMicrobial.fasta
> Reference Bin file
> []
> Tabular Report Column LabelsShort name
> HTML Report templatetemplates.html_report
>
>
>
>
> The other bug:
>
> 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy
> installs that have a prefix so that needs adjustment:
>
> $(".add-librarydataset").click(function() {
> var link = $(this);
> $.ajax({
> url: "/visualization/list_libraries",
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Tool param type "library_data"
Hi Damion, This change here https://bitbucket.org/galaxy/galaxy-central/pull-request/639/fix-for-librarydatasettoolparameter/diff might fix it. Thanks for reporting the issue, Sam On Thu, Jan 15, 2015 at 3:42 PM, Aysam Guerler wrote: > Hi Damion, > > I will look into this. > > Thanks, > Sam > > On Thu, Jan 15, 2015 at 3:30 PM, Dooley, Damion > wrote: > >> Hi, >> >> Almost! >> >> def get_initial_value( self, trans, context, history=None ): >> >> in /lib/galaxy/tools/parameters/basic.py under class >> LibraryDatasetToolParameter( ToolParameter ) gets past the error. Now a >> popup with "Grid failed" appears, with an OK button that cleanly exits (see >> attached). So I guess that part is still broken unless there is more to >> the input parameter setup. I had tested with >> >> >> >> I do like your better solution though, esp. if above control can't be >> primed with the desired library or folder. >> >> d. >> >> >> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC >> Centre for Disease Control >> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada >> >> From: James Taylor [ja...@jamestaylor.org] >> Sent: Thursday, January 15, 2015 12:53 AM >> To: Dooley, Damion >> Cc: galaxy-...@lists.bx.psu.edu >> Subject: Re: [galaxy-dev] Tool param type "library_data" >> >> It was only ever used for one tool that I know of, but we should make >> it work since we try to never break backward compatibility. If you add >> the 'history=None' kwarg is that sufficient to fix the problem? >> >> However, I think a better solution to this problem is to build it into >> dataset parameters. Anywhere a dataset can be provided it should be an >> option to provide a library dataset. Then one could imagine an option >> to restrict to only library datasets and a specific library. >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool param type "library_data"
Hi Damion, I will look into this. Thanks, Sam On Thu, Jan 15, 2015 at 3:30 PM, Dooley, Damion wrote: > Hi, > > Almost! > > def get_initial_value( self, trans, context, history=None ): > > in /lib/galaxy/tools/parameters/basic.py under class > LibraryDatasetToolParameter( ToolParameter ) gets past the error. Now a > popup with "Grid failed" appears, with an OK button that cleanly exits (see > attached). So I guess that part is still broken unless there is more to > the input parameter setup. I had tested with > > > > I do like your better solution though, esp. if above control can't be > primed with the desired library or folder. > > d. > > > Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre > for Disease Control > 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada > > From: James Taylor [ja...@jamestaylor.org] > Sent: Thursday, January 15, 2015 12:53 AM > To: Dooley, Damion > Cc: galaxy-...@lists.bx.psu.edu > Subject: Re: [galaxy-dev] Tool param type "library_data" > > It was only ever used for one tool that I know of, but we should make > it work since we try to never break backward compatibility. If you add > the 'history=None' kwarg is that sufficient to fix the problem? > > However, I think a better solution to this problem is to build it into > dataset parameters. Anywhere a dataset can be provided it should be an > option to provide a library dataset. Then one could imagine an option > to restrict to only library datasets and a specific library. > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fw: Re: galaxy server file upload problem
Hi Johngui, Can you open the console in your web browser and look at the url to which the file was posted to? Also please take a look into the Galaxy configuration file (config/galaxy.ini or universe_wsgi.ini) and try to find out to what the nginx_upload_path is set to. Thanks, Sam On Wed, Nov 19, 2014 at 8:16 PM, 홍종희 wrote: >Thanks for your reply Danon > > > > I have tried to setup local galaxy-server in production mode > > > > The error that I mentioned occurred when I tried to upload file from my > pc to local galaxy server( galaxy server is also installed in same pc ) > > > > and my galaxy server is at the root of the domain ( http://127.0.0.1:8080 > ) > > > > the attached file is screenshot of error and the other attached file is > my nginx configuration file > > > > Thanks for your effort in helping me > > > > Regards > > Jonghui > > > > - Original Message - > > *From:* Dannon Baker [dannon.ba...@gmail.com] > > *To:* 홍종희 [h...@syntekabio.com] > > *Cc:* Galaxy Dev [galaxy-...@lists.bx.psu.edu] > > *Sent:* Wed , November 19, 2014 23:19 PM > > *Subject:* Re: [galaxy-dev] galaxy server file upload problem > > > Hi Johngui, > > Can you specify which request is 404'ing -- the exact URL that's being > attempted? > > And, can you provide a little more of your nginx configuration? Is galaxy > being served at the root of the domain? > > -Dannon > > On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 < h...@syntekabio.com > wrote: > >> Hi galaxy-dev members >> >> >> >> Recently we're trying to setup the galaxy server in a production mode. >> >> >> >> Everything seems to be ok >> >> >> >> but when I tried to upload a file it shows error message like this >> >> >> >> Failed: Not found(404) >> >> >> >> I found one thread in galaxy-dev fourn about this one >> >> >> >> It says that it's because of change in proxy server configuration >> >> >> >> So I set exactly what was written in Galaxy wiki about nginx >> configuration related to proxy setting like below >> >> >> >> set $dst /api/tools; >> >> >> >> Should I change some oher configuration ? >> >> >> >> Any kind of suggestion would be welcomed >> >> >> >> Thanks >> >> Regards >> >> Jonghui >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
