ike it has an equivalent to the “nativeSpecification”
param like pbs-dramaa does. Have you had any experience with PBS-python vs.
PBS-drmaa? I’d be open to switching if the latter turns out to be more
reliable/flexible.
Cheers,
Sandra
From: SAPET, Frederic
Sent: Friday, 30 August 2019 5:52 PM
: parse error – I had configured a basic job_conf.xml to test with galaxy,
but it seems it was too basic. Are you perchance able to provide an example of
your job_conf.xml for reference?
Thanks,
Sandra
From: SAPET, Frederic via galaxy-dev
mailto:galaxy-dev@lists.galaxyproject.org>>
Sent: Wed
into the pbs-python installer script to hunt
down the relevant variables.
Re: parse error – I had configured a basic job_conf.xml to test with galaxy,
but it seems it was too basic. Are you perchance able to provide an example of
your job_conf.xml for reference?
Thanks,
Sandra
From: SAPET, Frederic via
Hi Sandra
We're running a Galaxy with PBS Pro as jobs scheduler.
I never had any problem with pbs-python however.
Here, for us, the PBS client is installed locally (on the VM that hosts Galaxy).
Are you sure that PBS is well installed ? Are you able to launch a simple PBS
script with the
d'origine-
De : SAPET, Frederic
Envoyé : mardi 20 août 2019 09:28
À : Galaxy-dev
Objet : RE: set up an asynchronous data source in galaxy
Hi,
I've tried with branch release_19.05 and dev (fetch yesterday from git)
Fred
-Message d'origine-
De : SAPET, Frederic via galaxy-dev
Envoyé
Hi,
I'm using bioblend to populate a library in galaxy. it's work well (bam and
vcf). But I have issues with some gff3.gz files.
For few of them (over 40 files) I see errors in the log.
If I upload that file (that fails with bioblend) it works using the upload tool
on the interface. It's
Hi,
I've tried with branch release_19.05 and dev (fetch yesterday from git)
Fred
-Message d'origine-
De : SAPET, Frederic via galaxy-dev
Envoyé : lundi 19 août 2019 17:19
À : Galaxy-dev
Objet : [galaxy-dev] set up an asynchronous data source in galaxy
Hi,
I'm trying to set up
Hi,
I'm trying to set up an asynchronous data source in galaxy.
I follow the examples that Helena provide here :
https://github.com/erasche/galaxy-data_source-examples/tree/master/flask
It's a success for synchronous modE.
But when I test the asynchronous mode, it fails.
from what I
I do :)
Thank you Dannon.
Fred
De : Dannon Baker
Envoyé : mardi 26 juin 2018 02:07:07
À : SAPET, Frederic
Cc : Hans-Rudolf Hotz; galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] MySQL errors and warnings with a fresh install of
Galaxy 18-05
-Rudolf Hotz [mailto:h...@fmi.ch]
Envoyé : jeudi 14 juin 2018 08:25
À : SAPET, Frederic ; Galaxy-dev
Objet : Re: [galaxy-dev] MySQL errors and warnings with a fresh install of
Galaxy 18-05
Hi Fred
Sorry, I don't have an answer I am just wondering: If you start from
'scratch', why don't you
Hi,
I try to install galaxy 18-05. My database backend is MysqL (5.7.11-4 Percona
Server)
I start from scratch (drop database, new directory with galaxy files fetched
with git)
So the database is first created when run.sh is used : :
Creating database for URI [mysql://
I see warnings
Hello
I try to use the from_dataset param.
I have a tabular file with two columns : sequence and ids
I would like to let users select some sequences, based on the ids.
But I would like to be able to access not only the sequences data, but
15:33
À : SAPET, Frederic <frederic.sa...@biogemma.com>
Cc : Galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Error at the end of a BWA job
Hi Frederic,
samtools couldn't be found, which is required for creating the bam index files
during the metadata sett
Hello
I've just installed BWA ((Galaxy Version 0.7.17.3) , Galaxy itself is On branch
release_17.09).
The first run is not a success.
I can see that the BAM is created, but job is tagged as fail (Unable to finish
job).
It looks like close to this issue:
: SAPET, Frederic <frederic.sa...@biogemma.com>
Cc : Laure QUINTRIC <laure.quint...@ifremer.fr>; Galaxy-dev
<galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Displaying tool select list according to user
On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic
<freder
to:p.j.a.c...@googlemail.com]
Envoyé : mercredi 20 septembre 2017 12:37
À : SAPET, Frederic <frederic.sa...@biogemma.com>
Cc : Laure QUINTRIC <laure.quint...@ifremer.fr>; Galaxy-dev
<galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Displaying tool select list according to u
[mailto:laure.quint...@ifremer.fr]
Envoyé : mercredi 13 septembre 2017 13:54
À : Peter Cock <p.j.a.c...@googlemail.com>; SAPET, Frederic
<frederic.sa...@biogemma.com>
Cc : Galaxy-dev <galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Displaying tool select list
Hi Laure,
There are others users (including me! ) that need this kind of function :
http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html
@Galaxy team:
Do we need to add an issue in GitHub ?
Do you think that it could be enabled one day ?
I think this something that could be nice
Hi
Same behavior for me.
Chrome (60.0) and IE (11.0.9600) are fine.
Fred
-Message d'origine-
De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part
de Jochen Bick
Envoyé : vendredi 25 août 2017 10:39
À : galaxy-dev@lists.galaxyproject.org
Objet : [galaxy-dev]
: SAPET, Frederic <frederic.sa...@biogemma.com>; Fernandez Edgar
<edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.
Hi Edgar, Frederic,
if you are using Apache as proxy for your Galaxy server, then you should
Hello,
Nice !
Thank you for the help.
Regards,
Fred
De : Fernandez Edgar [mailto:edgar.fernan...@umontreal.ca]
Envoyé : jeudi 15 juin 2017 16:41
À : SAPET, Frederic <frederic.sa...@biogemma.com>; galaxy-...@bx.psu.edu
Objet : RE: [galaxy-dev] new installation galaxy-17.05 - Uncaught
Hi
Same for me.
But It looks like to be related with tools installed via the toolshed (Ie :
bedtools, emboss, blast+ suite...).
My own tools seem to be ok.
Just like you Edgar, nothing in the log...
Fred
De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part
de
Great!
Thank you.
Fred
De : Dannon Baker [mailto:dannon.ba...@gmail.com]
Envoyé : mercredi 7 juin 2017 15:02
À : SAPET, Frederic <frederic.sa...@biogemma.com>;
galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] Paste/Fetch data, indicate filename before download
data (d
Hi,
I forgot to set again apache_xsendfile = True for my last tests,
So it appears that the "real" solution was to deactivate the SELinux mode.
I hope it will help somebody if they run into the same problem.
Fred
-Message d'origine-
De : SAPET, Frederic
Envoyé : mercredi
Hello,
I have also the same needs !
Would it be possible to enable Cheetah conditionnals within the tag ?
Something like this :
#if ($__user_email__.endswith('biogemma.com'))
#else
#end if
Fred
De : galaxy-dev
Chilton [mailto:jmchil...@gmail.com]
Envoyé : mardi 7 février 2017 18:56
À : SAPET, Frederic <frederic.sa...@biogemma.com>
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07
Sorry for the delay in responding - are yo
it would be nice.
Thank you.
Fred
De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part
de SAPET, Frederic
Envoyé : mercredi 24 août 2016 17:19
À : galaxy-dev@lists.galaxyproject.org
Objet : [galaxy-dev] Issue when using xsendfile with galaxy release_16.07
Hello
I'm
Hello
Despite the last update made to the file lib/galaxy/jobs/runners/drmaa.py I
still need to modify this file in order to truncate the job name to 15
characters.
I replace jobName=ajs.job_name by jobName=ajs.job_name[:15], (line 135).
The line 396 (job_name =
Hello
I'm trying the latest Galaxy (git status gives me : # On branch release_16.07)
Within the database directory, I've create a symbolic link :
tmp -> /tmp
But if this symbolic link is active, I'm unable to import an history using the
"Import from file" link.
Here is the error :
Hello
I'm trying the latest Galaxy (git status gives me : # On branch release_16.07)
I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web
server proxy, and apply all methods described here :
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
apache_xsendfile =
Hello
I'm trying the latest Galaxy (git status gives me : # On branch release_16.07)
I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web
server proxy, and apply all methods described here :
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
apache_xsendfile =
Hello
When I try to upload a file, I can see this error in the log file :
/softs/bioinfo/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:450:
Warning: Incorrect datetime value: '2016-03-29 07:25:29.220Z' for column
'update_time' at row 32
On the interface, the upload job
Hello
Using the previous version of Galaxy (before the 16.01) we were able to use PBS
Pro as job management system.
It was ok using PBS (/opt/pbs/12.2.4.142262) and DRMAA (pbs-drmaa-1.0.17).
This only thing to do was to truncate the job name that Galaxy send to PBS.
Indeed, in the file
you for the wiki.
Fred
-Message d'origine-
De : John Chilton [mailto:jmchil...@gmail.com]
Envoyé : mercredi 2 mars 2016 21:20
À : SAPET, Frederic <frederic.sa...@biogemma.com>
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] Tool Visibility feature
I have fixed
Hello
I'm trying to set up this feature :
https://wiki.galaxyproject.org/Admin/Config/Access%20Control
it seems that some files have been moved from : lib/galaxy/tools/filters/ to
lib/galaxy/tools/toolbox/filters/
by the way, when I uncomment " user_tool_filters =
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