Re: [galaxy-dev] Central German Galaxy User Group Meeting 2
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).
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@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 -------------------------------------------
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_work...
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/tutori... 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#g... Ciao, Bjoern
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).
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@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
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). https://github.com/common-workflow-language/common-workflow-language Best wishes, *Kristian On 8. Jan 2019, at 17:59 , Björn Grüning <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>> 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_work... 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/tutori... 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#g... Ciao, Bjoern 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). 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@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 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
participants (3)
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Björn Grüning -
Matthias Bernt -
Peters, Kristian