[mailto:jmchil...@gmail.com]
Envoyé : November-25-14 12:07 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] galaxy with torque
I am not sure we have a walkthrough for Torque specifically - but if you have
Galaxy up and running and you can qsub commands to torque
/torque/lib/libtorque.so
python scripts/scramble.py -e pbs_python
Cordialement / Regards,
Edgar Fernandez
De : Rémy Dernat [mailto:remy...@gmail.com]
Envoyé : December-02-14 11:49 AM
À : Fernandez Edgar
Cc : John Chilton; galaxy-...@bx.psu.edu
Objet : Re: Re : [galaxy-dev] galaxy with torque
Sorry
[mailto:jmchil...@gmail.com]
Envoyé : January-21-15 9:34 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] galaxy and torque - resource allocation
Was hoping someone with an actual torque cluster would respond. I think the way
you would configure this might be for instance might
, Fernandez Edgar wrote:
Actually, here’s what I came up with :
diff users.py ARCHIVES/users.py_20150205_9.28.18
23c23
q = sa.select( ( sa.func.date(
galaxy.model.User.table.c.create_time ).label( 'date' ),
---
q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date
with the arrow
going up constantly.
Do you think it’s an apache configuration error or galaxy or both?
Cordialement / Regards,
Edgar Fernandez
De : Nate Coraor [mailto:n...@bx.psu.edu]
Envoyé : January-22-15 10:10 AM
À : Fernandez Edgar
Cc : John Chilton; galaxy-...@bx.psu.edu
Objet : Re: [galaxy
Hello gents,
I started this new thread because I have a showstopper for my installation of
galaxy.
Here's my situation:
1. I have a galaxy server that has internet access.
2. My galaxy server is also my torque server and my only torque submit
node.
3. I have three torque
Hello Nate,
I just tried the modal upload dialog and it says File exceeds 2GB. Please use
FTP client.
Is there a way to increase that file size limitation?
Cordialement / Regards,
Edgar Fernandez
De : Nate Coraor [mailto:n...@bx.psu.edu]
Envoyé : January-22-15 12:02 PM
À : Fernandez Edgar
Cc
sincere apologies.
Cordialement / Regards,
Edgar Fernandez
De : Fernandez Edgar
Envoyé : January-22-15 12:35 PM
À : 'Nate Coraor'
Cc : John Chilton; galaxy-...@bx.psu.edu
Objet : RE: [galaxy-dev] galaxy and torque - resource allocation
Hello Nate,
I just tried the modal upload dialog and it says File
Good morning Gents,
I hope everyone is well.
I was wondering if it's possible to share data on Galaxy without all the users
downloading the data to their history.
Let me explain, teachers will be sharing data with their students.
And the students will need to work with that specific data.
Rasche [mailto:e...@tamu.edu]
Envoyé : January-22-15 3:05 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] show stopper for my galaxy installation
The tool to fetch data isn't being run on your submit node but instead on the
cluster, which is the problem.
It's a fairly
-22-15 3:05 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] show stopper for my galaxy installation
The tool to fetch data isn't being run on your submit node but instead on the
cluster, which is the problem.
It's a fairly easy to solve problem:
* In your job_conf
Hello gents,
I just installed "FASTQ Groomer tool" for the teachers to try it out and I've
been getting the following error than I do not understand:
galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is:
/home/galaxy/galaxy-prod/database/job_working_directory/000/756
Hello gents,
I hope everyone is doing ok...
I'm in need of your help so badly it's a little bit urgent:
So my galaxy wasn't used in a while but the last time everything was working
well:
1. The web-site was functional
2. The local handler upload the files locally on the master
3.
De : Josh Woodring [mailto:woodring.jos...@gmail.com]
Envoyé : September-17-15 11:14 AM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] need help badly
Hi Edgar,
I am a pretty big newbie to Galaxy but I have had similar problems on my Dev
build with grabbing outputs from
Hello gents,
I hope everyone is doing ok...
I'm in need of your help so badly it's a little bit urgent:
So my galaxy wasn't used in a while but the last time everything was working
well:
1. The web-site was functional
2. The local handler upload the files locally on the master
3.
dring.jos...@gmail.com]
Envoyé : September-17-15 12:34 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] need help badly
Hi Edgar,
Hm, I haven't gotten it to work but galaxy is supposed to support looking in
the working directory for the file. Its likely for reasons simila
Hello Gents,
So someone asked me to install the package Prokka on Galaxy.
I did and everything went well!
However, the following error comes up, when they try to work with Prokka:
Fatal error: Exit code 2 ()
[tbl2asn] This copy of tbl2asn is more than a year old. Please download the
current
[mailto:bjoern.gruen...@gmail.com]
Envoyé : September-29-15 8:10 AM
À : Fernandez Edgar; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] not sure what I can do about this...
Hi Edgar,
please download the latest version of tbl2asn from here:
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program
sues for us.
On Tue, Sep 29, 2015 at 9:24 AM Peter Cock
<p.j.a.c...@googlemail.com<mailto:p.j.a.c...@googlemail.com>> wrote:
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
<edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
> Hello Björn,
: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: May-26-16 3:32 AM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>; Nate Coraor
<n...@bx.psu.edu>
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] not sure what I can do about this...
Sorry Edgar,
It looks like something els
Technologies de l'Information et de la Communication
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
• Bur. : 1-514-343-6111 poste 16568
From: Martin Čech [mailto:mar...@bx.psu.edu]
Sent: January-25-16 9:33 AM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu
S
: input error or Microsoft
Azure.
Cheers!
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
• Bur. : 1-514-343-6111 poste 16568
From: Fernandez Edgar
Sent: May-18-16 2
: gzopen64
Thanks for your assistance!
Cheers,
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
• Bur. : 1-514-343-6111 poste 16568
From: Fernandez Edgar
Sent: May-19
-GAUDRY, bureau X-210
I Bur. : 1-514-343-6111 poste 16568
-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: May-24-16 2:29 PM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] not sure what I can do
Hey Guys,
Hope everyone is doing well.
So I’m back at galaxy v16.01
I’m having a small problem.
My python system version is 2.6.6
So I installed python version 2.7.8 from Software Collection Library release
1.2 packages for Oracle Linux 6
l'Information et de la Communication
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
I Bur. : 1-514-343-6111 poste 16568
-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Sent: May-24-16 5:40 PM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>
Cc:
Hello gents!
I’ve successfully got my version 16.04 up and running and everything is still
there (user, groups roles, data and tools).
Unfortunately , I’m still having a problem with deleting a user. I’ve purge him
and then I deleted him.
but, he still shows up in my list of users as "purged".
tion et de la Communication
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
• Bur. : 1-514-343-6111 poste 16568
From: Martin Čech [mailto:mar...@bx.psu.edu]
Sent: September-08-16 12:30 PM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu
Subject: Re: [ga
Hello,
I have installed prokka, perl and bioperl in my Galaxy's ToolShed.
However, my users are getting this error during execution of prokka:
Can't locate Bio/Root/Version.pm in @INC (@INC contains: /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
l'Information et de la Communication
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
• Bur. : 1-514-343-6111 poste 16568
From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola
Soranzo
Sent: October-07-16 3:14 PM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>;
Hey Guys,
I need your help understanding what’s happening with velvet devteam revision
08256557922f.
After installing it, velvet was giving me the following error:
galaxy.jobs.handler WARNING 2016-10-20 12:15:11,986 (1599) Tool
'toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0'
PAVILLON ROGER-GAUDRY, bureau X-210
• Bur. : 1-514-343-6111 poste 16568
From: Fernandez Edgar
Sent: October-31-16 11:40 AM
To: galaxy-...@bx.psu.edu
Subject: [galaxy-dev] galaxy - velvet devteam revision 08256557922f
Hey Guys,
I need your help understanding what’s happening with velvet devteam
l'Information
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
* Bur. : 1-514-343-6111 poste 16568
From: SAPET, Frederic [mailto:frederic.sa...@biogemma.com]
Sent: June 15, 2017 10:36 AM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu
Subject: RE: [galaxy-de
Hello gents,
I would greatly appreciate some help configuring my new installation of galaxy
18.05.
I found most of the configuration I needed but I'm missing the following
configuration in green.
Here is my galaxy 17.05:
[galaxy@esilbac3a ~]$ diff galaxy-17.05/config/galaxy.ini
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