New subject: Central German Galaxy User Group Meeting 2

8 Jan 2019

      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_work...
die scheinen planemo zu nutzen.
Waere mal eine passende Frage fuer galaxy-dev@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@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@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).

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

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%60 (replace USERNAME) or
`git
clone https://github.com/bioconda/bioconda-recipes%60
(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
)

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@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@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
-------------------------------------------

Re: [galaxy-dev] Central German Galaxy User Group Meeting 2