[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

[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: 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: 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: 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

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: 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

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

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] 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] 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] 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 $

[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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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

Hi all, *Devon* is correct -the old data library UI under Admin menu is still in place (because it has some features perceived as important to some admins). However majority of users and most of the admins are using the interface under 'Shared Data' I hope and the old UI is deprecated since 15.10

Re: [galaxy-dev] regarding tool dependencies

a system on > several popular Linux configurations would be greatly appreciated! At the > moment, I have abandoned the idea of setting up Galaxy in my lab, due to > time-consuming configuration problems... hopefully, we can re-try in the > future. > > Many thanks once more, >

Re: [galaxy-dev] Last stable galaxy Release 16.10 or 17.01 ?

Hello, 16.10 is the latest release however release of 17.01 is imminent and will probably happen early next week. The release_17.01 branch is what usegalaxy.org runs for the past few weeks without any big issues. The choice is yours but updating to release_17.01 now is alright I think as along as

Re: [galaxy-dev] Upgrade migration scripts

Hi Matthias, DB migrations need only to be run when there is a change in DB schema in between the releases. That is not the case between 16.10 and 17.01 so there is no migration to be run. When there is a migration to run, the startup process of Galaxy will abort and you will be presented with a

Re: [galaxy-dev] ImportError and Project life cycle

Hi Matthias, what version of Galaxy are you running? The tool you have installed seems to support only new Galaxies that have Conda dependency resolution enabled. We are currently in the middle of the transition of the Galaxy's ecosystem to this new dependency manager so there are rough edges

Re: [galaxy-dev] regarding tool dependencies

Hello Nir, the tool publishing process looks like this: tools for Galaxy are contributed by developers like you to the Tool Shed https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some tools have dependencies,

Re: [galaxy-dev] Tools using Galaxy's Python library?

Hi folks, the two of the Galaxy-born libraries have sources at our GitHub: https://github.com/galaxyproject/gops https://github.com/galaxyproject/sequence_utils Any improvements or PyPI-readiness work are welcome. Best, Martin On Tue, Jan 31, 2017 at 7:08 AM Peter Cock

Re: [galaxy-dev] Can't downgrade database.

Makis, you need to run the downgrade command (sh manage_db.sh downgrade --version=129) from the folder with the newer Galaxy. The old one does not have the downgrading scripts. Thanks for using Galaxy. Martin On Tue, Jan 17, 2017 at 7:33 AM Makis Ladoukakis wrote: >

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] 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] 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] 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] 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

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

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] 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] Help wanted: setting up a production server

Hi Steve, make sure to check out https://wiki.galaxyproject.org/Events There are 2 extensive admin trainings going to happen in near future. November in Salt Lake City and February in Melbourne. Martin On Fri, Oct 7, 2016 at 4:23 PM Steve Cassidy wrote: > Hi all, >

Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

Hi Martin, > > Thanks! > > The first link doesn't really work...upon going to github it gave me 404. > After I explored a bit more > it says itself that it may not work now. :-( > > However the second one looks quite promising! > > Cheers, > Rui > > On Mon, Sep 26,

Re: [galaxy-dev] samtools

Hi Rui, you can install the following suite which includes about a dozen of wrapped samtools. https://toolshed.g2.bx.psu.edu/view/devteam/suite_samtools_1_2/5b673ccc8747 Martin On Mon, Sep 26, 2016 at 11:05 AM Beginner TI wrote: > I did see that if I click each

Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

Hi Rui, there is no 'mirror' button to obtain Main's toolset yet, but many pieces are in place to help you with this. Please see the following answers for guides and links: https://biostar.usegalaxy.org/p/11338/ https://biostar.usegalaxy.org/p/19660/ Thanks, Martin On Mon, Sep 26, 2016

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

> > It’s 15.03. > > > > Regards, > > Dineli > > > > *From:* Martin Čech [mailto:mar...@bx.psu.edu] > *Sent:* Tuesday, September 13, 2016 10:31 PM > *To:* Amarathunga A. Dineli Karunath; galaxy-...@bx.psu.edu > *Subject:* Re: [galaxy-dev] Trimmomatic to

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

for your feedback. We don’t have any javascript errors… > > > > Stephanie > > > > *De : *Martin Čech <mar...@bx.psu.edu> > *Date : *mardi 13 septembre 2016 16:36 > *À : *Stephanie Le Gras <sleg...@igbmc.fr>, " > galaxy-dev@lists.galaxyproject.org"

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

Hello Stephanie, I have just tested this on 16.07 and on `dev` branch of Galaxy and it works for both in my case. Can you please check the browser's console for javascript errors? Thanks, Martin On Tue, Sep 13, 2016 at 10:22 AM Stephanie LE GRAS wrote: > Hi there (again), >

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

Hi Dineli, what version of Galaxy do you have installed? thanks Martin On Tue, Sep 13, 2016 at 10:27 AM Amarathunga A. Dineli Karunath < dineli_karunathil...@nuhs.edu.sg> wrote: > Hi, > > I have a local galaxy instance and have installed many tools from the > galaxy tool shed. Recently I have

Re: [galaxy-dev] delete user and all trace of user

; *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la Communication > > *Université de Montréal* > > > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568* > &g

Re: [galaxy-dev] delete user and all trace of user

Hi Edgar, there is no built-in way in Galaxy to remove a user completely. 'Deleting' just flips the flag in the DB and 'purging' is related to their data/histories. You need to access the DB directly if you want to completely remove a user. Beware that there might be constraints/relations

Re: [galaxy-dev] Testtoolshed status

This has been fixed now, thanks Steve for the report and sorry for the trouble. Martin On Fri, Sep 2, 2016 at 10:20 AM Dave Bouvier wrote: > Steve, > > Thank you for reporting this issue, we've determined a potential cause > and are working to correct it. > > - > Dave Bouvier

Re: [galaxy-dev] error on startup

previous instance of reports running, and I'm not sure what to check as > far as ports. > our AWS guy said it might be an issue with AWS but I don't know enough > about all this to confirm (or to know how to confirm). > > thanks for your help. > > On Thu, Sep 1, 2016 at 1:39 PM,

Re: [galaxy-dev] error on startup

; this is the first time we have that issue though, and the instance has > been running just fine until now. I don't think we've changed anything. > > On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech <mar...@bx.psu.edu> wrote: > >> Hi Cris, >> >> what `host` and `

Re: [galaxy-dev] error on startup

Hi Cris, what `host` and `port` is in your reports.ini config file? This stacktrace would point at something already running at the same port. Martin On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas wrote: > Galaxy admins, > One of you has probably seen the below error

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] Adding packages to depot.galaxyproject.org

Peter: depot is something we plan on maintaining and providing as a service as long as Galaxy. The cargo-port we will also expand in future (eg to provide dynamic fallback at installation time. It is the right place to put your mira backups (and any other packages you care about in recipes).

[galaxy-dev] Fwd: New galaxy parameter type

forwarding to the list -- Forwarded message - From: Katherine Beaulieu <katherine.beaulieu...@gmail.com> Date: Fri, Jul 15, 2016 at 3:45 PM Subject: Re: [galaxy-dev] New galaxy parameter type To: Martin Čech <mar...@bx.psu.edu> Thanks Peter, I will look into that.

Re: [galaxy-dev] New galaxy parameter type

Katherine please disregard my answer, I probably misread your question. :) M. On Fri, Jul 15, 2016 at 3:05 PM Peter Cock wrote: > Did you mean parameter as in input field shown > to the user? Like a combobox or text field? > > Since this happened to come up earlier

Re: [galaxy-dev] New galaxy parameter type

Hi Katherine, an example of a datatype addition can be seen in this PR: https://github.com/galaxyproject/galaxy/pull/2452 You need to define a class and teach it to sniff files of your defined type (with a doctest) and how to generate peek for the datatype's datasets in history. Let us know if

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

Hi Cristel, for a start I please have a look at http://planemo.readthedocs.io/en/latest/writing_advanced.html#test-driven-development and let us know if you have further questions. The documentation regarding this is a still bit scarce, I am sorry. Martin On Mon, Jul 11, 2016 at 3:24 PM Cristel

Re: [galaxy-dev] showing progress on running tasks

the progress instead of Galaxy estimating that. > > If instance, if the tool know it has 5 stages, it can report back to > Galaxy 20,40,60,80,and 100 % complete. > > I know this is complex but could be a nice feature. > > Please excuse any typos -- Sent from my iPhone > > O

Re: [galaxy-dev] showing progress on running tasks

Hi Ryan, This is a fairly complex problem because the length of the run depends most often on input size, job algorithms, and computational capacity all of which are quite difficult to estimate. We have discussed it before and one of the ways to approach this is to gather statistics from as many

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

The correct link is this: http://galaxy-dev.fmi.ch/tool_ runner/biomart?type=text=Homo%20sapiens%20genes%20% 28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/ 7ee294b9ae51a27f1e7ed96e712c5792? On Wed, Jun 8, 2016 at 11:33 AM Martin Čech <mar...@bx.psu.edu> wrote: > This l

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

t; http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1 > > > > Hans-Rudolf > > > On 06/08/2016 04:36 PM, Martin Čech wrote: > >

Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?

Hello Malcolm, encoded_id is a database row id that has been ran through this method ( https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__init__.py#L46) using the 'secret' from galaxy.ini config. You should be able to do something like this in the mako:

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

Hello Hans-Rudolf, What version of Galaxy are you using? Can you please share a specific URL you were sent to that returns a 404? thanks M. On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz wrote: > Hi all > > Please allow me to come back to this old problem: > > On

Re: [galaxy-dev] Tool shed tools, manual dep installation

wrong though. > > Thanks, > > DT > > -- > David Trudgian Ph.D. > Computational Scientist, BioHPC > Lyda Hill Department of Bioinformatics > UT Southwestern Medical Center > Dallas, TX 75390-9039 > Tel: (214) 648-4833 > > From: Martin Čech [mailto:mar.

Re: [galaxy-dev] Tool shed tools, manual dep installation

Hi David, one thing that you might be missing is that the wrapper for the infosec-approved version might not exist yet (you would have to adapt the older shed-wrapped version if there were any relevant changes). But this largely depends on what software you want to use. Besides that your flow

Re: [galaxy-dev] Request help to configure local galaxy in Git

Hi Manonanthini, Windows is not a supported platform for Galaxy and we do not have any official tutorials, tests or even proofs that it can be done. I recommend you run a virtual machine with a Linux image and install Galaxy there. Depending on what you want to do you can grab our pre-populated

Re: [galaxy-dev] automatic adding of a tab in a fastq header

gt; I'm glad to see your suggested fix has already been applied to > the Galaxy repository so should be in the next stable release. > > Thank you! > > Peter > > (Also thank you Martin, Nicola, Dan, etc) > > > On Tue, Mar 22, 2016 at 8:43 PM, Martin Čech <mar...@bx.psu.ed

Re: [galaxy-dev] automatic adding of a tab in a fastq header

Thank you very much for solving this Fabien, The PR with your fix has been created here: https://github.com/galaxyproject/galaxy/pull/1985 Martin On Mon, Mar 21, 2016 at 5:43 PM fmareuil wrote: > Hi Peter, > > I worked on it today and I found the reason of this bug. In

Re: [galaxy-dev] Please help fix toolshed repository: trtr

n I clone the repo, I don't see that folder: > >hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr > > Lance > > Martin Čech wrote: > > > Hi Lance, > > it seems the whole .git/ folder got accidentally uploaded there and it > causes trouble. I recomme

Re: [galaxy-dev] Using forms to collect user info at registration

Hello Peter, you are right, this seems broken, sorry about that. I have created an issue to track the resolution of this bug: https://github.com/galaxyproject/galaxy/issues/1937 Thank you for reporting it. Martin On Wed, Mar 16, 2016 at 10:16 AM Peter Briggs

Re: [galaxy-dev] Please help fix toolshed repository: trtr

Hi Lance, it seems the whole .git/ folder got accidentally uploaded there and it causes trouble. I recommend using the direct mercurial access ( https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the folder, commit the change and push it to the TS repository. Please let me know how it

Re: [galaxy-dev] Galaxy Conference

Hello Scott, have you seen the schedule at https://gcc16.sched.org/ ? The trainings are all listed, described, and categorized there, it should help you decide what to attend. >From my experience in addition to scientists there are many admins and developers attending the conference so you

Re: [galaxy-dev] copy/import shared history

this “copy shared > history” function. Thanks for your information. > > Best > > Le-Shin > > > On Feb 16, 2016, at 1:02 PM, Martin Čech <mar...@bx.psu.edu> wrote: > > Hi LW, > > 1) The described 'copy' feature works well for me on usegalaxy.org. > However t

Re: [galaxy-dev] bx-python issue with intersect and subtract tools

Hello Richard, this issue has been solved, if you update the tool it should work as expected. Details are available here: https://biostar.usegalaxy.org/p/15974/ Thank you for using Galaxy Martin On Tue, Dec 1, 2015 at 5:28 PM Poole, Richard wrote: > Hi all, > > I just

Re: [galaxy-dev] Working on the admin interface: JS vs Mako

Hi, Galaxy is implementing frontend with the help of these libraries: https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/libs Notably the MV-paradigm is being implemented in Backbone. Good examples of applications/pieces that are written in JS are at

Re: [galaxy-dev] Get data via the cloud?

Hi Scott, Galaxy can retrieve data from any publicly available URL. Just paste the URL into the upload modal using the 'paste/fetch data'. This probably won't work with some of the services as they won't serve you content without visiting their site. But it works with e.g. dropbox if you add

Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

Hi Amos, what Galaxy are you using and where are you seeing these messages? thanks Martin On Thu, Jan 28, 2016 at 2:56 PM Raphenya, Amogelang wrote: > Hi All, > > Is there a faster way to upload or load large datasets into galaxy history > without using FTP? > > I tried

Re: [galaxy-dev] errors installing tool dependencies...

> My Sincere Salutations, > > > > *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la Communication > > *Université de Montréal* > > > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. :

Re: [galaxy-dev] errors installing tool dependencies...

bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568* > > > > > > *From:* Fernandez Edgar > *Sent:* January-25-16 11:11 AM > *To:* 'Martin Čech' <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu > *Subject:* RE: [galaxy-dev] errors installing tool dependencies...

Re: [galaxy-dev] Want to Contribute in galaxy project

Hi Manish, thank you very much for your interest in Galaxy project! I would first look here to check the beginner's dev overview: https://wiki.galaxyproject.org/Develop/GettingStarted And once you feel somewhat comfortable you can check the beginner friendly issues on GitHub here:

Re: [galaxy-dev] errors installing tool dependencies...

cola Soranzo [mailto:nicola.sora...@gmail.com > <nicola.sora...@gmail.com>] *On Behalf Of *Nicola Soranzo > *Sent:* January-25-16 12:05 PM > *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca> > <edgar.fernan...@umontreal.ca>; Martin Čech <mar...@bx.psu.edu> > &l

Re: [galaxy-dev] configuration management, tool shed and tool revisions

Hello Steve, Galaxy project's efforts in automating tool installations are mostly represented by the following Ansible playbook ( https://github.com/afgane/galaxy-tools-playbook) and a role ( https://github.com/galaxyproject/ansible-galaxy-tools). We plan on improving that tracked at:

Re: [galaxy-dev] Sample tracking / external services - still supported?

Hello Matthias, As you correctly identified the original implementation, in spite of being present in the Galaxy distribution, is treated as deprecated. However I know about three sample tracking implementation based on Galaxy's old sample tracking. - *TRON Mainz*

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