Re: [galaxy-dev] problem with local toolshed

Hello Vincent, This looks like an encoding problem we we can fix. Could you please try the following patch? https://gist.github.com/martenson/22f6efc7cd577ea6af85a11694091d5f Thanks, Martin On Wed, Aug 24, 2016 at 5:17 AM Vincent Cahais wrote: > Hello, > > I cannot use my

Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

ivate" that is in the bottom of the uninstall page. Hope this helps and please let us know when it does not. Thanks, Martin On Wed, Oct 19, 2016 at 9:29 AM Pierre Lindenbaum < pierre.lindenb...@univ-nantes.fr> wrote: > On 10/19/2016 03:23 PM, Martin Čech wrote: > > Hi Pierre, > >

Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

niv-nantes.fr> wrote: > On 10/19/2016 03:36 PM, Martin Čech wrote: > > Hi Pierre, > > > > It seems that instead of uninstalling you de-activated the repository. > > I would uninstall the repository again. > > admin > manage installed tools > there is no t

Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

Hi Pierre, how old is your Tool Shed? When was the last time a tool installation from it succeeded? thanks M. On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum < pierre.lindenb...@univ-nantes.fr> wrote: Hi all, I got a "Internal Server Error" ==> "KeyError: 'tool_panel_section' " when I'm

Re: [galaxy-dev] Changing Tool Shed URL

Thank you very much for sharing Youssef. Very helpful. Martin On Fri, Oct 21, 2016 at 10:20 AM Youssef GHORBAL wrote: > Hello, > > Two other tables need to be adapated (they reference tool_id) > Table “job" and table “workflow_step” > > Youssef

Re: [galaxy-dev] Is there demand for rate limiting in Galaxy?

Max: you are correct, the dev branch is what would be the best to develop against. Also feel free to open PR with work in progress at any point. I am sure you will get useful feedback. Thank you for using Galaxy, Martin On Wed, Nov 23, 2016 at 5:40 AM Maximilian Friedersdorff

Re: [galaxy-dev] Elastic Bean Stalk

Hi Ryan, if you are planning to use Galaxy on AWS I recommend you to have a look at the CloudMan (https://wiki.galaxyproject.org/CloudMan). It will help you orchestrate the instances and scale to meet the needs of your users. It has been a while since I used the EB, but generally when scaling

Re: [galaxy-dev] Restart Galaxy without interruption

Hi Gildas, the approach which Main Galaxy takes is as described by Nate in the exercise document linked by Laure. Exerpt here: "In addition, you can gracefully restart the uWSGI Galaxy process with sudo supervisorctl signal HUP gx:galaxy. uWSGI is configured to start Galaxy in a "master" process

Re: [galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

Hi Floreline, I am afraid you cannot choose the name of the dataset in advance. You can however change it once it is in your history by accessing the edit menu under the pencil icon. Would that help? thank you for using Galaxy p.s. The pencil icon you mention in the upload dialog seems to not

Re: [galaxy-dev] Login message

Hi Timo, the message is defined in lib/galaxy/webapps/galaxy/controllers/user.py as variable REQUIRE_LOGIN_TEMPLATE . It does not seem configurable but you could modify it directly. Thanks for using Galaxy Martin On Wed, Mar 29, 2017 at 11:32 AM Timo Janßen wrote: > Hi,

Re: [galaxy-dev] Login message

Timo: Yes please, github issues are the right place for these ideas. thanks Martin On Wed, Apr 5, 2017 at 10:32 AM Timo Janßen <timo.jans...@gwdg.de> wrote: > On 03/29/2017 05:36 PM, Martin Čech wrote: > > the message is defined in lib/galaxy/webapps/galaxy/cont

Re: [galaxy-dev] Search Tool Shed

was the Privacy Badger browser plugin. > Might it be that data is exchanged with the toolshed page? > > Anyway, I disabled the plugin and the page works. > > Best, > Matthias > > On 08.03.2017 16:20, Martin Čech wrote: > > Hi Matthias, > > > > it is suppo

Re: [galaxy-dev] Search Tool Shed

Hi Matthias, it is supposed to open an iframe in the right panel with view of MTS categories for browsing. Do you see a warning icon in the right of your browser's URL bar? I think I saw this before when there was https/https mismatch. How does your config/tool_sheds_conf.xml look like? Do you

Re: [galaxy-dev] Shared Data Library, large number of files

> > > > On Wed, Mar 8, 2017 at 10:29 AM, Martin Čech <mar...@bx.psu.edu> wrote: > > Daniel: > > what version is your Galaxy? > > Martin > > On Wed, Mar 8, 2017 at 12:40 PM D K <danielforti...@gmail.com> wrote: > > I've copied and pasted

Re: [galaxy-dev] Shared Data Library, large number of files

screenshot of the relevant > window. I also tried logging in as a non-admin user and had the same issue. > In this Galaxy instance are 5 data libraries, each with about 150 > individual folders, and each folder has a variable number of fastq.gz files. > > Thanks! > > On Thu, Mar 2

Re: [galaxy-dev] Shared Data Library, large number of files

http://collabedit.com/xcx5b > > Thanks! > > On Wed, Mar 8, 2017 at 11:04 AM, Martin Čech <mar...@bx.psu.edu> wrote: > > Can you please share your '/client/galaxy/scripts/layout/menu.js' file > with me? (e.g. using https://gist.github.com or similar). > > thanks > &

Re: [galaxy-dev] Galaxy User IDs and Group IDs

Hi Rob, especially on a new Galaxy they tend to because every Galaxy table has its own id series which is in turn encoded with the same secret. So when you create your first user and your first group, they will have the same id (1). Same with first history, first dataset etc. iow: Galaxy objects

Re: [galaxy-dev] Additional Information about users in the API

Hi Milen, I don't think Galaxy exposes what you ask for through an API and a PR to make it do so is certainly welcomed. Please note that this information (about other users) should be only exposed to an admin. Additionally is there a reason why you are gathering these stats through an API and

Re: [galaxy-dev] Additional Information about users in the API

Stephan, Milen, lately Galaxy undergoes DB migrations very rarely and if so it usually just adds tables/columns in a very clear manner. API should shield you from any changes breaking your DB script but to be honest I would not expect any unless you are gathering data on some complex object

Re: [galaxy-dev] Problems with the test tool shed?

Done, seems up now. Thanks for the report. M. On Tue, Oct 17, 2017 at 2:22 PM Von Kuster, Greg wrote: > Hi all, > > I’m wondering if the TTS can be restarted. I’ve been seeing this > of-and-on all afternoon. > > Thanks! > > Galaxy > The Test Tool

Re: [galaxy-dev] Enable viewing of large HTML files

Hi Peter, I believe the 1MB is hard coded in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/managers/hdas.py#L222 and cannot be configured. That said you can change it on your instance, I have also opened an issue to allow configuring this value.

[galaxy-dev] Release of Galaxy 17.09

Dear Galaxy Fans, The release* of Galaxy **17.09* is out. Thanks to the #usegalaxy committers and you, our community! *Full *release * notes: * https://docs.galaxyproject.org/en/master/releases/17.09_announce.html Highlights: *Singularity - *Tool execution using the HPC-friendly container

[galaxy-dev] The Galaxy release 18.05 is out

Dear Community, We are happy to release Galaxy 18.05. Many thanks to committers and you, the community. Enjoy the on time release and please let us know if you face any issues. The release notes are available at https://docs.galaxyproject.org/en/release_18.05/releases/18.05_announce.html Thanks

Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

Hi Hans-Rudolf, the problem is that the 18.05 release is missing the viz static files in the proper folder. To be precise /config/plugins/visualizations/*/static needs to be copied to /static/plugins/visualizations/*/static To fix: (make sure you have node 8.x.x and not newer) $ cd client $

Re: [galaxy-dev] galaxy upgrade 18.05 problem

Hi Matthias, this used to be a (deprecated) symlink, which we removed in 18.05. You need to change your proxy as can be seen here: https://github.com/galaxyproject/ansible-galaxy-extras/pull/206/files The release notes announcement:

Re: [galaxy-dev] User Registration Error

Hi Dallas, this really does look like a permissions issue, could you please double check who owns that file? Alternatively you can just remove all the *.pyc in Galaxy's folders, it will be recreated with proper permissions during the first run. Thanks for using Galaxy, M. On Tue, Jan 16, 2018

Re: [galaxy-dev] Updating Bioblend on existing Galaxy installation

The biostar thread corresponding to this question is at https://biostar.usegalaxy.org/p/26849/. M. On Thu, Feb 22, 2018 at 5:26 PM Lachlan Musicman wrote: > Sorry all, moving this Q over to biostars. > > -- > "The antidote to apocalypticism is *apocalyptic civics*.

Re: [galaxy-dev] Installing Tool Dependencies

kages. > > > > Thank you! > > Tom > > > > *From:* Martin Čech > *Sent:* Monday, July 16, 2018 12:42 PM > *To:* Tom Misilo > *Cc:* galaxy-...@bx.psu.edu > *Subject:* Re: [galaxy-dev] Installing Tool Dependencies > > > > Hello Tom, > > > > that

Re: [galaxy-dev] Installing Tool Dependencies

Hello Tom, that page is very very outdated and I wouldn't trust it. Do you have any specific tools from that list that are giving you trouble? If not then I would ignore it completely. Majority of the tools are now installed through the Toolshed and dependencies are auto-managed by Galaxy's own

Re: [galaxy-dev] From Paste to uWSGI

Another recently updated resource for uwsgi is the training slides: https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi/uwsgi.html#1 M. On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs wrote: > Hello Jochen > > I'm not aware of a tutorial but here are some observations from my

Re: [galaxy-dev] question regarding GALXY software

Hi David, Galaxy does not add much on top of what the tools you need to run require so if you have a laptop that you can run your analysis on you can run the analysis using Galaxy also. Martin ‪On Tue, Apr 10, 2018 at 11:41 AM ‫דויד קורנספן [David Kornspan]‬‎ < davi...@moag.gov.il> wrote:‬ > >

Re: [galaxy-dev] FTP service for galaxy with external authentication via SAML using shibboleth

Hi all, with the 'chunked and resumable uploads' PR in place ( https://github.com/galaxyproject/galaxy/pull/5516) the resiliency of the built-in uploader should be pretty high, especially on browser like Chrome. This feature will make it to 18.05 release. M. On Tue, Apr 17, 2018 at 2:20 PM

Re: [galaxy-dev] GVL/Galaxy ver 18.01 instance error: R_COMM channel basic get exception: [Errno 32] Broken pipe

Hi Leon, list, this issue is now tracked here: https://github.com/galaxyproject/cloudlaunch/issues/140 Martin On Mon, Mar 26, 2018 at 5:14 AM Leon Parker wrote: > We just stood up our first ever Genomics Virtual Lab appliance and used it > to spool up a Galaxy

[galaxy-dev] Release of Galaxy 18.01

Dear Galaxy Fans, The release of Galaxy 18.01 is out. Thanks to the Galaxy committers and you, our community! Full release notes: https://docs.galaxyproject.org/en/release_18.01/releases/18.01_announce.html *Highlights:* *Performance and User Experience Improvements* We made Galaxy more lively

Re: [galaxy-dev] Search box in tools menu / uncomplete wrappers list

Hi Sarah, toolpanel search in Galaxy is configurable. Due to limited space the default number of results shown is 20 so if there are more you are not going to see them. You can also change weights of various search attributes or use ngram search. Please see the config options explained in the

Re: [galaxy-dev] Get Data and 'xlsx'

Hi all, I can confirm this file is sniffed as `format: blastxml` on usegalaxy.org, which is surely wrong. I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/6849 M. On Wed, Oct 10, 2018 at 2:11 PM D K wrote: > Sure, I've attached a sample xlsx file and my

Re: [galaxy-dev] [External] Copying files to FTP upload directory

Hi Keith, your message is not bouncing, it shows here: http://dev.list.galaxyproject.org/ Your setup seems correct to me, does Galaxy have permission to read files in the given folders? Also Galaxy will auto-create folders if set the `user_library_import_dir` to be the same as ftp and use

[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

Eric: I recommend https://help.galaxyproject.org/ for your question, it might reach a better audience there. Paula: I believe you can unsubscribe here: https://lists.galaxyproject.org/lists/galaxy-dev.lists.galaxyproject.org/ Regards, Martin On Wed, May 22, 2019 at 12:49 PM Paula Berrutti

[galaxy-dev] Re: Nginx+Shibboleth+UCSC

Hi Martin, I am sorry you did not get any responses on the list, the reason for it is most probably the lack of our experience with Shibboleth, which seemed to be the main cause of the issues you were facing. To answer your last question: the `display_as` is the path to put on the proxy allow

[galaxy-dev] Re: Error when installing from toolshed

Hi Nancy, what versions of Galaxy did you update from and to? Please check if you have cookies enabled in your browser. Martin On Wed, Jul 31, 2019 at 9:45 AM Nancy Ide wrote: > Hello > > I am suddenly (after pulling a new version of galaxy) unable to install > from the toolshed. The error

[galaxy-dev] Re: Error when installing from toolshed

ur galaxy instance for the > LAPPS Grid, which is using version 19.01. > > On Jul 31, 2019, at 6:34 PM, Martin Čech wrote: > > Hi Nancy, > > what versions of Galaxy did you update from and to? Please check if you > have cookies enabled in your browser. > > Martin > > On

[galaxy-dev] Re: Error when installing from toolshed

that the > repository queue was loaded and has 0 elements). When I click on the > “Galaxy Main Toolshed” button I can select one of the options but nothing > happens. This is also true now on our jetstream instance. > > > On Jul 31, 2019, at 7:02 PM, Martin Čech wrote: > > Wo

[galaxy-dev] Re: Error when installing from toolshed

When I tried to pull from github it complained that some of my”untracked” > files would be overwritten. I did a git stash but 3 files still were said > to be overwritten, and I simply deleted those. The pull then went on > uneventfully. > > On Jul 31, 2019, at 6:53 PM, Martin Čech wro

[galaxy-dev] Re: Problem with uploading data

Hi Rodrigo, I am not aware of any known issues with the rule based uploader that you seem to be using. Please provide details about what Galaxy you are trying this on and what error(s) you are getting. Thanks, Martin On Fri, Nov 22, 2019 at 1:58 PM Rodrigo Machado via galaxy-dev <

[galaxy-dev] Re: To implement a one-click test for a Galaxy tool.

Hi Jin, Galaxy has a functionality to generate tool tours using the tool's own test data. See https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/webhooks/demo/tour_generator This functionality is enabled e.g. on usegalaxy.eu so you might want to check it out and see if it fits your

[galaxy-dev] Re: (null):// header in visualisation links (IGV etc.)

I don't know your setup but maybe you could serve Galaxy on a different port without Apache/ssl to test. M. On Wed, Apr 14, 2021 at 11:58 AM wrote: > Uff, I'll try that, though it will take some time since I have to figure > out what in my apache config belongs to the proxying and what to the >

[galaxy-dev] Re: (null):// header in visualisation links (IGV etc.)

Lubos, do you have an opportunity to disable the proxy for a bit? So we can narrow down the suspects. Martin On Wed, Apr 14, 2021 at 11:22 AM Lubos Klucar wrote: > Dear Helena, > > thanks a lot, but I'm afraid this is not the case - 'RequestHeader' is > set as described. > > It should be

<    1   2