Hi,
just to mention that deseq2-1-8-2 (requiring r-3-2-1) also installs fine!
Best regards,
Hans
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Hi Marius,
I bow to your efforts in appreciation - it seems to install without flaws!!
I tried the new cairo-1-12-14 and then r-3-2-1 in a frest postgresqldb/galaxy
instance … everything got installed and shows the green label ;-)
requirements on top of Mac OS Xcode/command line tools are:
- gf
Hi Bob,
you could write a special visualisation for your specific datatype. This
does not work with the eyeball, but with the visualisation button
associated to every dataset.
For a few visualisation examples please see the following links:
*
https://github.com/galaxyproject/galaxy/tree/dev/conf
Good afternoon,
I am trying create a display module for a special binary datatype. When
someone requests to view the output file in the History using the eyeball it
will kick off my code to create an HTML display in the Galaxy center section.
I am looking at binary.py but I am not sure if th
Everything is working fine now.
I experienced problems : I forgot to delete some files this made a conflict.
If anybody needs, the python script has to be in the bin folder of the computer
not in the HOME folder (I've made a mistake with the tilde)
Thanks again, normally I will not bother you an
Hi Makis,
as a small pointer, please have a look at the ansible playrole we provide:
https://github.com/galaxyproject/ansible-galaxy-extras
or the Galaxy Docker Image:
https://github.com/bgruening/docker-galaxy-stable
all steps are described here and can be reused.
Cheers,
Bjoern
Am 04.12.201
Awesome Marius, thank you very much for looking into this! M.
On Fri, Dec 4, 2015 at 12:30 PM Marius van den Beek
wrote:
> Hello Hans (and other OS X users),
>
> I hope that the last remaining problem should be fixed now.
> There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on
Hello Hans (and other OS X users),
I hope that the last remaining problem should be fixed now.
There is a new revision of package_r_3_2_1 and package_cairo_1_12_14 on the
toolshed.
Make sure you get package_cairo_1_12_14 first when you upgrade.
The underlying problem was that cairo was missing the
I've written up my experiences in a blog:
http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/
The only Galaxy side changes were the ones mentioned on the Scaling page.
The Bad Gateway message means that Apache can't talk to the uWSGI so what
is the state of uWSGI?
Are you using superv
On Fri, Dec 4, 2015 at 2:16 PM, Peter Cock wrote:
> On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE wrote:
>> Ok i did not saw it.
>> I runned it with ./ and it worked fine. It gave me the same answer you gave
>> me earlier.
>>
>> Olivier
>
> Excellent :)
>
> So, this matches what I found - as l
On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE wrote:
> Ok i did not saw it.
> I runned it with ./ and it worked fine. It gave me the same answer you gave
> me earlier.
>
> Olivier
Excellent :)
So, this matches what I found - as long as I changed to the Wolf PSORT
directory first, runWolfPsort
Ok i did not saw it.
I runned it with ./ and it worked fine. It gave me the same answer you gave me
earlier.
Olivier
-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com]
Envoyé : vendredi 4 décembre 2015 12:40
À : Olivier CLAUDE
Cc : galaxy-dev@lists.galaxyproject.org
On Fri, Dec 4, 2015 at 11:19 AM, Olivier CLAUDE wrote:
> Hi Peter,
> Thanks for all.
>
> ...
>
>>
>> What happens if you try to do this:
>>
>> $ cd /path/you/put/wolfpsort
>> $ ./runWolfPsortSummary animal
>> <~/repositories/pico_galaxy/test-data/four_human_proteins.fasta
>>
>
> It gives me :
>
>
Hi Peter,
Thanks for all.
$ arch
>x86_64
$ uname -a
>Linux LM1166 3.16.0-38-generic #52~14.04.1-Ubuntu SMP Fri May 8
09:43:57 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
$ which perl
>/usr/bin/perl
$ perl -v
> This is perl 5, version 18, subversion 2 (v5.18.2) built for
x
Hi Olivier,
First of all, let's double check what kind of machine you are running,
in case that gives us some clues:
$ arch
$ uname -a
Let's double check which Perl you have,
$ which perl
$ perl -v
$ /usr/bin/perl -v
NOTE: You have to pipe the input file into this tool, it does
not take the in
Hello again,
I cannot launch it manually neither. It gives me the same error… :
>runWolfPsortSummary animal test.fasta
>Can't locate fastafmt/GetOptWarnHandler.pm in @INC (you may need to install
>the fastafmt::GetOptWarnHandler module) (@INC contains: /etc/perl
>/usr/local/lib/perl/5
It is uwsgi that I am trying but with apache. Could you let me know what
changes you made to the configuration of Galaxy?
Thank you,
Makis
Date: Fri, 4 Dec 2015 10:01:56 +0200
Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.
Hello Hans,
I'm not sure if it would help to use the pre-compiled binaries,
as you would still need some of the underlying libraries for building
R packages. We're not far from having this fixed ... there is a newer
revision of R on the main toolshed,
that nevertheless will (probably) fail because
Hi,
I now learned that R-3.2.2 binaries for Mac OS X are available
(https://cran.r-project.org/bin/macosx/) - could that be a potential help for
R-related problems in galaxy on Mac OS X?
Cheers,
Hans
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Hi Makis, I recently implemented something like this using uWSGI with a
nginx frontend. Would you consider using uWSGI instead of your current
approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" wrote:
> Sorry for bumping my own question but I didn't get any replies. Has anyone
> succesfully instal
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