Re: [galaxy-dev] conda problem

2017-08-31 Thread Björn Grüning 
Hi Matthias,

conda-build only supported 80 chars limit for a long time. This has
fixed and all new packages don't have this problem.

So hopefully this PR will fix it:

https://github.com/bioconda/bioconda-recipes/pull/5912

Cheers,
bjeorn

On 31.08.2017 17:19, Matthias Bernt wrote:
> Dear list,
> 
> When running rmarkdown_wgcna I get the following error in the logs:
> 
> PaddingError: Placeholder of length '80' too short in package
> bioconda::r-wgcna-1.51-r3.3.1_0.
> The package must be rebuilt with conda-build > 2.0.
> 
> The command that seems to lead to this is:
> 
> Executing command:
> /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda
> create -y --name mulled-v1-3bfe8da4ed798836281cc963619917
> 317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0
> r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2
> r-htmltools=0.3.5 r-wgcna=1.51
> 
> Any ideas?
> 
> Best,
> Matthias
> 
> 
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Re: [galaxy-dev] unipept visualization

2017-08-31 Thread Nicola Soranzo 

Hi Matthias,
that should be fixed on dev already by pull request: 
https://github.com/galaxyproject/galaxy/pull/4522


Cheers,
Nicola

On 31/08/17 16:30, Matthias Bernt wrote:

Hi Sam,

I tried on 17.05 and dev without any success. Any idea where I could 
start debugging?


Best,
Matthias

On 30.08.2017 18:23, Aysam Guerler wrote:

Hey Matthias,

I noticed that this visualization has already been added and should 
be working in release 17.05 and a d3_hierarchy file. Its documented 
at 
https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations/unipept.


Example files are available here:
https://github.com/unipept/unipept-visualizations/tree/master/examples/data 



Now here is the issue I noticed, once you upload one of these example 
files, you need to select the file in the history, click on the 
pencil icon and change the datatype to 'd3_hierarchy' before 
attempting to visualize it. You cannot select the correct datatype in 
the upload view. I will test this a little bit more and fix it if 
necessary for the next release.


I hope this helps.
Thanks again.

On Mon, Aug 28, 2017 at 4:23 AM, Matthias Bernt > wrote:


Hi Sam,

thanks for the answer. So far I have not configured anything, I was
hoping that it works out of the box :).

Could you point me to some documentation where the setup is 
explained?


Best,
Matthias

On 25.08.2017 19 :05, Aysam Guerler wrote:

Hi Matthias,

Have you added the visulization to Charts or the regular Galaxy
visualization framework? If it is the latter please make sure
that you correctly specified the datatype in your XML file. Your
visualization should than appear in the drop-down list in the
history.

Thanks,
Sam

On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt  >> wrote:

 Dear list,

 I can not get the wonderful unipept visualization to work
on our
 Galaxy instance (a test instance on the dev branch). I get
the message:
 "Unfortunately we could not identify a suitable plugin"

 The file I try to visualize was generated by unipept
(pept2lca) and
 is of format d3_hierarchy.

 Could someone tell me if I need to install / configure
something to
 get this running?

 Thanks a lot.

 Best,
 Matthias


 P.S. This might be also of interest for others, since this
 visualization is used in the Metaproteomics tutorial of the
GTN.


 --
 ---
 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  >, 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
 Administrative Geschäftsführerin/ Administrative Managing
Director:
 Prof. Dr. Heike Graßmann
 ---
___
 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/

>



--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ

Re: [galaxy-dev] unipept visualization

2017-08-31 Thread Matthias Bernt 

Hi Sam,

I tried on 17.05 and dev without any success. Any idea where I could 
start debugging?


Best,
Matthias

On 30.08.2017 18:23, Aysam Guerler wrote:

Hey Matthias,

I noticed that this visualization has already been added and should be 
working in release 17.05 and a d3_hierarchy file. Its documented at 
https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations/unipept.


Example files are available here:
https://github.com/unipept/unipept-visualizations/tree/master/examples/data

Now here is the issue I noticed, once you upload one of these example 
files, you need to select the file in the history, click on the pencil 
icon and change the datatype to 'd3_hierarchy' before attempting to 
visualize it. You cannot select the correct datatype in the upload view. 
I will test this a little bit more and fix it if necessary for the next 
release.


I hope this helps.
Thanks again.

On Mon, Aug 28, 2017 at 4:23 AM, Matthias Bernt > wrote:


Hi Sam,

thanks for the answer. So far I have not configured anything, I was
hoping that it works out of the box :).

Could you point me to some documentation where the setup is explained?

Best,
Matthias

On 25.08.2017 19 :05, Aysam Guerler wrote:

Hi Matthias,

Have you added the visulization to Charts or the regular Galaxy
visualization framework? If it is the latter please make sure
that you correctly specified the datatype in your XML file. Your
visualization should than appear in the drop-down list in the
history.

Thanks,
Sam

On Fri, Aug 25, 2017 at 5:25 AM, Matthias Bernt  >> wrote:

 Dear list,

 I can not get the wonderful unipept visualization to work
on our
 Galaxy instance (a test instance on the dev branch). I get
the message:
 "Unfortunately we could not identify a suitable plugin"

 The file I try to visualize was generated by unipept
(pept2lca) and
 is of format d3_hierarchy.

 Could someone tell me if I need to install / configure
something to
 get this running?

 Thanks a lot.

 Best,
 Matthias


 P.S. This might be also of interest for others, since this
 visualization is used in the Metaproteomics tutorial of the
GTN.


 --
 ---
 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  >, 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
 Administrative Geschäftsführerin/ Administrative Managing
Director:
 Prof. Dr. Heike Graßmann
 ---
 ___
 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/

>



-- 


---
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 , www.ufz.de

[galaxy-dev] conda problem

2017-08-31 Thread Matthias Bernt 

Dear list,

When running rmarkdown_wgcna I get the following error in the logs:

PaddingError: Placeholder of length '80' too short in package 
bioconda::r-wgcna-1.51-r3.3.1_0.

The package must be rebuilt with conda-build > 2.0.

The command that seems to lead to this is:

Executing command: 
/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda 
create -y --name mulled-v1-3bfe8da4ed798836281cc963619917
317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0 
r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2 
r-htmltools=0.3.5 r-wgcna=1.51


Any ideas?

Best,
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.be...@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
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
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/