Re: Central German Galaxy User Group Meeting 2

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Re: Central German Galaxy User Group Meeting 2

Matthias Bernt
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_workflow_tests.sh

die scheinen planemo zu nutzen.

Waere mal eine passende Frage fuer [hidden email] ...


> - 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 <[hidden email]
>> <mailto:[hidden email]>> 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 <[hidden email]
>>>> <mailto:[hidden email]> <mailto:[hidden email]>> 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,
>> [hidden email] <mailto:[hidden email]>, 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,
[hidden email], 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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Re: Central German Galaxy User Group Meeting 2

Björn Grüning-3
Hi Kristian,

Am 08.01.19 um 17:40 schrieb Matthias Bernt:

> 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_workflow_tests.sh 
>
>
> die scheinen planemo zu nutzen.
>
> Waere mal eine passende Frage fuer [hidden email] ...

Yes, planemo is the way to go I think.

There is some documentation in
https://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html#testing-the-workflow-recommended

In https://github.com/usegalaxy-eu/workflow-testing/ you can look at
many examples. Despite the broken Jenkins server, which is running out
of disc-space all of these workflows actually passing the tests :)

>
>> - 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.

Jupp.
https://quay.io/organization/biocontainers

>> - 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.

This works for all OpenMS and Seqan tools. It does not produce
super-duper quality tools, but they tend to work. Matthias, all our
OpenMS wrappers are generated with that.

Description here:

https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms#generating-openms-wrappers

Ciao,
Bjoern

> Gruesse,
> Matthias
>
>> Viele Grüße, *Kristian
>>
>>
>>> On 7. Jan 2019, at 17:46 , Matthias Bernt <[hidden email]
>>> <mailto:[hidden email]>> 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 <[hidden email]
>>>>> <mailto:[hidden email]> <mailto:[hidden email]>> 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,
>>> [hidden email] <mailto:[hidden email]>, 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
>>
>>
>
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Re: Central German Galaxy User Group Meeting 2

Peters, Kristian
Hi Matthias,

just want to add that there are also initiatives for a Common Workflow Language [1].

Galaxy is also supported and is in alpha-stage (whatever that means).


Best wishes, *Kristian



On 8. Jan 2019, at 17:59 , Björn Grüning <[hidden email]> wrote:

Hi Kristian,

Am 08.01.19 um 17:40 schrieb Matthias Bernt:
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_workflow_tests.sh die scheinen planemo zu nutzen.
Waere mal eine passende Frage fuer [hidden email] ...

Yes, planemo is the way to go I think.

There is some documentation in https://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html#testing-the-workflow-recommended

In https://github.com/usegalaxy-eu/workflow-testing/ you can look at many examples. Despite the broken Jenkins server, which is running out of disc-space all of these workflows actually passing the tests :)

- 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.

Jupp.
https://quay.io/organization/biocontainers

- 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.

This works for all OpenMS and Seqan tools. It does not produce super-duper quality tools, but they tend to work. Matthias, all our OpenMS wrappers are generated with that.

Description here:

https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms#generating-openms-wrappers

Ciao,
Bjoern

Gruesse,
Matthias
Viele Grüße, *Kristian


On 7. Jan 2019, at 17:46 , Matthias Bernt <[hidden email] <mailto:[hidden email]>> 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 <[hidden email] <mailto:[hidden email]> <mailto:[hidden email]>> 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,
[hidden email] <mailto:[hidden email]>, 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



Dr. Kristian Peters
IPB-Halle, AG Massenspektrometrie & Bioinformatik
Weinberg 3
06120 Halle (Saale)
kpeters[at]ipb-halle.de
Tel. +49 (0)345 5582 1475
Fax. +49 (0)345 5582 1409


___________________________________________________________
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/