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 galaxy-dev@lists.galaxyproject.org ...
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 <m.be...@ufz.de
<mailto:m.be...@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 <sneum...@ipb-halle.de
<mailto:sneum...@ipb-halle.de> <mailto:sneum...@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.be...@ufz.de <mailto:m.be...@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
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