galaxy-dev January 2019

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13 participants
15 discussions

Re: [galaxy-dev] Central German Galaxy User Group Meeting 2
by Matthias Bernt 09 Jan '19

09 Jan '19

Hi Kristian, > - Die <test>, <output tests> oder <assert_stdout> funktionieren nur für > ein einziges Tool? Genau. > Wenn man einen ganzen Workflow testen muss, dann kann > man das wie machen? Wir hatten dazu mal wft4galaxy benutzt, evtl. gibts > noch was besseres? Habe ich selber noch keine Erfahrung mit gemacht. Kannst zum Beispiel mal bei usegalaxy-eu schauen: https://github.com/usegalaxy-eu/workflow-testing/blob/master/.travis.yml https://github.com/usegalaxy-eu/workflow-testing/blob/master/run_galaxy_wor… die scheinen planemo zu nutzen. Waere mal eine passende Frage fuer galaxy-dev(a)lists.galaxyproject.org ... > - Erzeugt PLANEMO sowohl eine Galaxy-XML als auch CONDA-rules? Nein, nur das Galaxy xml. > - Wenn ich CONDA Regeln erzeuge, wie gelangt das automatisch nach > BIOCONTAINER? Wenn dein recipe in bioconda gemerged wurde wird automatisch ein container mit erzeugt .. soweit ich weiss. > - Hast du schon einmal von der Common Tool Description (CTD) gehört? > Damit kann man mit einer Tool-Beschreibung Tools für verschiedene > Workflow-Systeme erzeugen. Weißt du ob das mittlerweile gut funktioniert? Davon habe ich noch nichts gehoert. Kannst du mir mal einen link schicken - taete mich interessieren. Gruesse, Matthias > Viele Grüße, *Kristian > > >> On 7. Jan 2019, at 17:46 , Matthias Bernt <m.bernt(a)ufz.de >> <mailto:m.bernt@ufz.de>> wrote: >> >> Hi, >> >> wir werden versuchen zumindest den Vormittag per skype zu uebertragen. >> Am besten einfach mich (mbatle) ab ca 8:45 mal anschreiben. >> >> Gruesse, >> Matthias >> >> On 05.01.19 11:50, Peters, Kristian wrote: >>> Hallo Matthias, >>> Januar ist bei mir sehr gefüllt und es sind noch ein paar wichtige >>> Sachen oben drauf gekommen. Daher hatte ich mich vorsichtshalber >>> nicht in den Doodle eingetragen. Vielleicht ist es möglich, per >>> Telefonkonferenz (Hangout, Skype) remote teilzunehmen? Das würde mir >>> viel Zeit am Dienstag ersparen. >>> Viele Grüße, *Kristian >>>> On 4. Jan 2019, at 19:40 , Neumann, Steffen <sneumann(a)ipb-halle.de >>>> <mailto:sneumann@ipb-halle.de> <mailto:sneumann@ipb-halle.de>> wrote: >>>> >>>> Hi Matthias, >>>> >>>> ich habe die Koordination von einem grösseren Antrag geerbt, >>>> und werde daher am Dienstag nicht nach Leipzig kommen können :-( >>>> >>>> Kristian hat in den letzten Wochen ebenfalls >>>> an einem Workflow für MetFrag gearbeitet, >>>> zu dem wir bis jetzt PhenoMeNal packaging haben. >>>> >>>> Gruss, >>>> Steffen >>>> >>>> >>>> On Fri, 2019-01-04 at 18:46 +0100, Matthias Bernt wrote: >>>>> Dear all, >>>>> >>>>> our meeting (workshop on building Galaxy tools and conda packages) >>>>> will >>>>> take place next Tuesday (Feb 8th). Below we compiled the most >>>>> important >>>>> informations for you. Just write an email if you have any further >>>>> questions. >>>>> >>>>> We are currently expecting the eight participants who registered >>>>> here: >>>>> https://dudle.inf.tu-dresden.de/7yxdfay2/. Let me know if you >>>>> changed >>>>> you plans. >>>>> >>>>> The meeting will take place in the KUBUS (Tagungsbüro 131) at the >>>>> UFZ. >>>>> How to reach the UFZ is described here: >>>>> https://www.ufz.de/index.php?de=34272 The KUBUS is in front of the >>>>> UFZ. >>>>> So you don't need to enter through the main gate. >>>>> >>>>> Plan: >>>>> >>>>> - We will start at 9:00. >>>>> - For the morning we plan to introduce you to the basics of >>>>> - building tools for Galaxy with planemo and >>>>> - building conda packages >>>>> - For lunch there is a "Kantine" at the UFZ. >>>>> - In order to practice the learned topics we planned to use the >>>>> afternoon as a kind of hackaton where you can (start to) build >>>>> your own Galaxy tool or conda package. We will be there for >>>>> questions >>>>> and introduce advanced topics as needed. >>>>> >>>>> Therefore it would be great if you 'bring' a tool of your choice, >>>>> eg >>>>> your own tool for wrapping, this could be e.g. a shell, R, or >>>>> python >>>>> script or some software package that can be compiled. >>>>> >>>>> In case that you don't have an idea we have prepared one or two >>>>> examples. >>>>> >>>>> Important: >>>>> >>>>> Since some of the required software is quite large we would like to >>>>> ask you to prepare a few things if possible (at least the first >>>>> point). >>>>> >>>>> 1. You will need a linux command line >>>>> >>>>> If your laptop runs Windows you could install VirtualBox and install >>>>> a >>>>> linux in this box. Linux images for VirtualBox that are ready to use >>>>> are >>>>> available, eg. >>>>> https://www.osboxes.org/ubuntu/#ubuntu-1804-vbox >>>>> >>>>> 2. Download and prepare the bioconda recipes repository >>>>> >>>>> - optional: create a fork of >>>>> https://github.com/bioconda/bioconda-recipes >>>>> - clone your fork or the main repository, i.e. either `git clone >>>>> https://github.com/USERNAME/bioconda-recipes` (replace USERNAME) or >>>>> `git >>>>> clone https://github.com/bioconda/bioconda-recipes` >>>>> >>>>> (see >>>>> >>>> https://bioconda.github.io/contrib-setup.html#git-and-github-one-time-setup >>>>> ) >>>>> >>>>> In the bioconda-recipes root directory call: >>>>> >>>>> ``` >>>>> ./bootstrap.py TEMPORARY_PATH_TO_WHERE_MINICONDA_SHOULD_BE_INSTALLED >>>>> ``` >>>>> >>>>> Replace TEMPORARY_PATH_TO_WHERE_MINICONDA_SHOULD_BE_INSTALLED with >>>>> some >>>>> path where miniconda can be installed. >>>>> >>>>> (see https://bioconda.github.io/contribute-a-recipe.html#test-locally >>>>> ) >>>>> >>>>> 3. Prepare planemo and Galaxy >>>>> >>>>> Install `planemo` via pip or conda as described here: >>>>> >>>>> (see https://planemo.readthedocs.io/en/latest/installation.html) >>>>> >>>>> Get a copy of the Galaxy sources: >>>>> >>>>> ``` >>>>> git clone -b release_18.09 >>>>> https://github.com/galaxyproject/galaxy.git >>>>> ``` >>>>> >>>>> We are looking forward to see you on Tuesday. >>>>> >>>>> Best, >>>>> Joerg and Matthias >>>>> >>>>> >>>>> >>>>> On 04.12.18 10:31, Matthias Bernt wrote: >>>>>> Dear all, >>>>>> >>>>>> we will meet on 8th of January at the UFZ in Leipzig. I reserved a >>>>>> room >>>>>> for 10 people (Tagungsbüro 131 KUBUS). There are still some places >>>>>> free, >>>>>> if you want to come and did not fill the dudle yet (or if you were >>>>>> unsure) I would like to ask you to add yourself -- in order to >>>>>> keep >>>>>> track on the number of attendees. >>>>>> >>>>>> We will send directions and all necessary informations before the >>>>>> meeting. >>>>>> >>>>>> Looking forward to see you. >>>>>> >>>>>> Cheers, >>>>>> Matthias >>>>>> >>>>>> >>>>>> On 30.11.18 15:56, Matthias Bernt wrote: >>>>>>> Gentle reminder to fill the dudle :) Currently we have only >>>>>>> three >>>>>>> entries. >>>>>>> >>>>>>> Cheers, >>>>>>> Matthias >>>>>>> >>>>>>> On 26.11.18 13:44, Matthias Bernt wrote: >>>>>>>> Dear all, >>>>>>>> >>>>>>>> since there was only little feedback on the last survey I will >>>>>>>> start >>>>>>>> another try to schedule the 2nd CGGUG meeting. The idea is to >>>>>>>> have a >>>>>>>> workshop on building Galaxy tools and conda packages (of course >>>>>>>> there >>>>>>>> will be also sufficient time for other discussions on the >>>>>>>> administration or use of Galaxy). >>>>>>>> >>>>>>>> Please fill in here until the end of the November: >>>>>>>> >>>>>>>> https://dudle.inf.tu-dresden.de/7yxdfay2/ >>>>>>>> >>>>>>>> Our preference would be the 17th in December :) >>>>>>>> >>>>>>>> Best, >>>>>>>> Matthias >>>>>>>> >>>>>>>> >>>>>>>> On 30.08.18 12:53, Matthias Bernt wrote: >>>>>>>>> Dear all, >>>>>>>>> >>>>>>>>> Joerg Fallman and myself agreed on a week early in December >>>>>>>>> for the >>>>>>>>> next meeting that will take place in Leipzig (at UFZ or >>>>>>>>> Bioinformatics@Uni-Leipzig): >>>>>>>>> >>>>>>>>> Feel free to mark preferred dates here: >>>>>>>>> >>>>>>>>> https://dudle.inf.tu-dresden.de/cggug2-date/ >>>>>>>>> >>>>>>>>> We will keep you posted. >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Matthias >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 22.08.2018 14:32, Matthias Bernt wrote: >>>>>>>>>> Dear all, >>>>>>>>>> >>>>>>>>>> it has been a while since our last meeting in Halle and we >>>>>>>>>> have >>>>>>>>>> thought about reanimating the meeting here in Leipzig >>>>>>>>>> (hopefully in >>>>>>>>>> September). >>>>>>>>>> >>>>>>>>>> Since building Galaxy tools and conda packages seemed to be >>>>>>>>>> topics >>>>>>>>>> that are of interest for many of you Joerg Fallmann, >>>>>>>>>> Stephanie >>>>>>>>>> Kehr, and myself thought that we could give a little >>>>>>>>>> workshop on at >>>>>>>>>> least one of these topics. >>>>>>>>>> >>>>>>>>>> If you are interested then just check one of the options or >>>>>>>>>> leave a >>>>>>>>>> comment here: https://dudle.inf.tu-dresden.de/cggug2/ >>>>>>>>>> >>>>>>>>>> We will try to find a date and room as soon as we have an >>>>>>>>>> approximate number of participants (poll will close on 29th >>>>>>>>>> of >>>>>>>>>> September). >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Matthias >>>>>>>>>> >>>>> >>>>> >>>> -- >>>> >>>> IPB Halle AG Massenspektrometrie & Bioinformatik >>>> Dr. Steffen Neumann http://www.IPB-Halle.DE >>>> Weinberg 3 Tel. +49 (0) 345 5582 - 1470 >>>> 06120 Halle +49 (0) 345 5582 - 0 >>>> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 >>> Dr. Kristian Peters >>> IPB-Halle, AG Massenspektrometrie & Bioinformatik >>> Weinberg 3 >>> 06120 Halle (Saale) >>> kpeters[at]ipb-halle.de <http://ipb-halle.de> <http://ipb-halle.de> >>> Tel. +49 (0)345 5582 1475 >>> Fax. +49 (0)345 5582 1409 >> >> -- >> >> ------------------------------------------- >> 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.bernt(a)ufz.de <mailto:m.bernt@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 >> ------------------------------------------- > > Dr. Kristian Peters > IPB-Halle, AG Massenspektrometrie & Bioinformatik > Weinberg 3 > 06120 Halle (Saale) > kpeters[at]ipb-halle.de <http://ipb-halle.de> > Tel. +49 (0)345 5582 1475 > Fax. +49 (0)345 5582 1409 > > -- ------------------------------------------- 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.bernt(a)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 -------------------------------------------

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sorry
by Matthias Bernt 08 Jan '19

08 Jan '19

Dear all, sorry for the last post .. accident. But it actually contained an interesting question: What are currently good approaches for testing workflows? Cheers and sorry again :(, 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.bernt(a)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 -------------------------------------------

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run.sh problem
by Matthias Bernt 08 Jan '19

08 Jan '19

Dear all, a colleague tries to run.sh on a Manjaro Linux and got the following error: ``` yarn run v1.12.3 $ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash gulp[12888]: ../src/node_contextify.cc:628:static void node::contextify::ContextifyScript::New(const v8::FunctionCallbackInfo<v8::Value>&): Assertion `args[1]->IsString()' failed. 1: 0x8daaa0 node::Abort() [gulp] 2: 0x8dab75 [gulp] 3: 0x90e2f7 node::contextify::ContextifyScript::New(v8::FunctionCallbackInfo<v8::Value> const&) [gulp] 4: 0xb5e71b [gulp] 5: 0xb606b2 v8::internal::Builtin_HandleApiCall(int, v8::internal::Object**, v8::internal::Isolate*) [gulp] 6: 0x6f20bcdbe1d /tmp/yarn--1546955496175-0.8677740791371564/node: line 3: 12888 Aborted (core dumped) "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/.venv/bin/node" "$@" error Command failed with exit code 134. info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command. ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help. Problem running Galaxy command []. Traceback (most recent call last): File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/bin/planemo", line 11, in <module> sys.exit(planemo()) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/cli.py", line 195, in handle_blended_options return f(*args, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/commands/cmd_serve.py", line 43, in cli galaxy_serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 22, in serve return _serve(ctx, runnables, **kwds) File "/home/henning/nextcloud/PhD/20190108-galaxy_workshop/galaxy/env/lib/python3.7/site-packages/planemo/galaxy/serve.py", line 54, in _serve raise Exception(message) Exception: Problem running Galaxy command []. ``` Would be great to have a suggestion... 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.bernt(a)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 -------------------------------------------

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Forgotten password
by Dalibor Miklík 07 Jan '19

07 Jan '19

Hello, recently I tried to login to my Galaxy account but, obviously, I forgot my password and I can't reset it because I didn't receive any email from the webpage. Can you please help me? Best regards Dalibor Miklik

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January 2019 Galactic News: Events (Admin Training, PAG, GSOC, GCC, GalaxyAdmins), Platforms, Pubs, Jobs, COTM!, Doc, Training, Tools, Releases and more!
by Mo Heydarian 04 Jan '19

04 Jan '19

Hello All, Happy New Year! The *January 2019 Galactic News* is here! This is a summary of what is going on in the Galaxy community. Here's what's happening: - Event News <https://galaxyproject.org/news/2019-01-galaxy-update/#event-news> - 2019 Galaxy Admin Training: Registration is still open! <https://galaxyproject.org/news/2019-01-galaxy-update/#2019-galaxy-admin-tra…> - Training topic nomination for GCC2019 Training extended through 15 January! <https://galaxyproject.org/news/2019-01-galaxy-update/#gcc2019-training-topi…> - Galaxy will be at the 2019 Plant and Animal Genome (PAG) conference <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-pag-2019> - Galaxy needs your Google Summer of Code Project suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-needs-your-goo…> - And GalaxyAdmins needs your topic suggestions <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxyadmins-needs-yo…> - 80 new publications <https://galaxyproject.org/news/2019-01-galaxy-update/#publications>, including several spectacular ones - Some most excellent Galaxy Platform News <https://galaxyproject.org/news/2019-01-galaxy-update/#galaxy-platforms-news>, including the *EGI Marketplace*. - The Contributor of the Month is ... Simon Gladman <https://galaxyproject.org/news/2019-01-galaxy-update/#new-galactic-blog-pos…> ! - 17 Open positions <https://galaxyproject.org/news/2019-01-galaxy-update/#whos-hiring> in 6 countries on 3 continents. - Doc, Hub, and Training Updates <https://galaxyproject.org/news/2019-01-galaxy-update/#doc-hub-and-training-…> covering RNA-Seq visualizations, BlockClust, cloud storage, cancer proteogenomics, and some introductory videos - ToolShed contributions <https://galaxyproject.org/news/2019-01-galaxy-update/#toolshed-contributions> - New releases <https://galaxyproject.org/news/2019-01-galaxy-update/#releases>: - Tripal Galaxy - connect Galaxy to your online database - BioBlend - a Python API for Galaxy and CloudMan - Planemo - utilities for building tools for Galaxy - And a bunch of other news <https://galaxyproject.org/news/2019-01-galaxy-update/#other-news> too See the newsletter for all of the details! Thanks for using Galaxy! Cheers, Mo Heydarian, on behalf of Galaxy

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galaxy-dev January 2019