[galaxy-dev] galaxy with torque

Hello all, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've contacted you a while back about installing galaxy and I've successfully done it on a redhat 6 server. I see myself in a situation where I need to utilise all my redhat servers (who are identical to the ser

Re: [galaxy-dev] galaxy with torque

 : John Chilton [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 com

Re: [galaxy-dev] galaxy with torque

scripts/scramble.py -e pbs_python. However, LIBTORQUE_DIR is empty. Once again, thank you in advance for all your help! Cordialement / Regards, Edgar Fernandez De : remy...@gmail.com [mailto:remy...@gmail.com] Envoyé : December-02-14 6:34 AM À : Fernandez Edgar; John Chilton Cc : galaxy

Re: [galaxy-dev] galaxy with 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

Re: [galaxy-dev] galaxy with torque

the near future, please feel free to tell me. I’m curious about your input on this. Once again, thank you so much! Cordialement / Regards, Edgar Fernandez De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : December-03-14 9:53 AM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re

Re: [galaxy-dev] galaxy with torque

...@gmail.com] Envoyé : December-03-14 9:53 AM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy with torque That handle id seems wrong... at least it is not what I am used to. It needs to match a server section specified in your galaxay ini file - usually this is a

Re: [galaxy-dev] galaxy with torque

d symbol: log_record Removing PID file handler0.pid Any suggestions is more than welcome since I have a lot of pressure to make this work. Thanks gents !!! Cordialement / Regards, Edgar Fernandez De : Nate Coraor [mailto:n...@bx.psu.edu] Envoyé : December-04-14 4:09 PM À : Fernandez Edgar Cc

Re: [galaxy-dev] galaxy with torque

ot;, line 93, in __restarter File "/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/update_repository_manager.py", line 133, in sleep File "/usr/lib64/python2.6/threading.py", line 137, in release : 'NoneType' object is not callable Please advise! Cordiale

[galaxy-dev] galaxy and torque - resource allocation

Hello gents, Hope everyone had a great holiday break! Wish you guys all the best for 2015! I have a couple of questions about how resources (CPU and memory) is allocated when you have a galaxy and torque installation. So I've setup torque with some default and maximum amount of CPU and memory

Re: [galaxy-dev] galaxy and torque - resource allocation

r Fernandez -Message d'origine- De : John Chilton [mailto:jmchil...@gmail.com] Envoyé : January-18-15 8:59 PM À : Fernandez Edgar Cc : galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy and torque - resource allocation Galaxy generally defers to the DRM (torque in your case) for dealing wi

Re: [galaxy-dev] galaxy and torque - resource allocation

-- De : John Chilton [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 f

Re: [galaxy-dev] galaxy and torque - resource allocation

eWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.91 Safari/537.36" ip_addr - - [22/Jan/2015:10:18:29 -0400] "GET /galaxy-prod/api/histories/5a0831c911c29227/contents HTTP/1.1" 200 - "http://esiservera.esi.umontreal.ca:8081/galaxy-prod/root"; "Mozilla/5.0 (X11;

Re: [galaxy-dev] galaxy and torque - resource allocation

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 : Fernande

Re: [galaxy-dev] galaxy and torque - resource allocation

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

[galaxy-dev] show stopper for my galaxy installation

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 com

Re: [galaxy-dev] show stopper for my galaxy installation

-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 you

Re: [galaxy-dev] show stopper for my galaxy installation

z De : Eric 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&

[galaxy-dev] data sharing without duplication?

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. Howeve

[galaxy-dev] galaxy report page - server error solution?

Hello guys, So I've been working on the Galaxy report page. It works fine however I'm using MySQL and I'm getting some server errors on some webpages. I found the solution: https://lists.galaxyproject.org/pipermail/galaxy-dev/2009-August/000641.html But can some please confirm the following:

Re: [galaxy-dev] galaxy report page - server error solution?

el( 'date' ), 425c425 < group_by=[ sa.func.year ( model.Job.table.c.create_time ), sa.func.month ( sa.func.date( model.Job.table.c.create_time ) ) ], --- >group_by=[ sa.func.date_trunc( 'month', sa.func.date( > model.Job

Re: [galaxy-dev] galaxy report page - server error solution?

On 02/05/2015 04:20 PM, 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' ), &g

Re: [galaxy-dev] galaxy report page - server error solution?

73c173 <group_by = [ sa.func.year ( model.Request.table.c.create_time ), sa.func.month ( sa.func.date( model.Request.table.c.create_time ) ) ], --- >group_by = [ sa.func.date_trunc( 'month', > sa.func.date( model.Request.table.c

[galaxy-dev] need help badly

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.

[galaxy-dev] need help badly

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.

Re: [galaxy-dev] need help badly

ent / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : September-17-15 9:44 AM À : galaxy-...@bx.psu.edu Objet : [galaxy-dev] need help badly 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

Re: [galaxy-dev] need help badly

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 the

Re: [galaxy-dev] need help badly

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 s

[galaxy-dev] not sure what I can do about this...

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 v

Re: [galaxy-dev] not sure what I can do about this...

üning [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_pr

Re: [galaxy-dev] not sure what I can do about this...

sues for us. On Tue, Sep 29, 2015 at 9:24 AM Peter Cock mailto:p.j.a.c...@googlemail.com>> wrote: On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar mailto:edgar.fernan...@umontreal.ca>> wrote: > Hello Björn, > > Thank you for answering! > When I installed Prokka from the Gala

[galaxy-dev] FASTQ Groomer tool

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 gal

Re: [galaxy-dev] FASTQ Groomer tool

Hello again, I installed today the tool : fastq_all_to_sanger I get the same SQL error with that one too. Any ideas guys? Thank you!!! Cordialement / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : November-04-15 8:58 AM À : 'galaxy-...@bx.psu.edu' Objet : [galaxy-dev] FAS

Re: [galaxy-dev] FASTQ Groomer tool

: Fernandez Edgar; galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] FASTQ Groomer tool Hi Edgar, you can try to restart Galaxy (both web and handler processes) and re-run the tool. Cheers, Nicola On 05/11/15 19:18, Fernandez Edgar wrote: Hello again, I installed today the tool : fastq_all_to_sanger

Re: [galaxy-dev] R: Re: FASTQ Groomer tool

until the restart. I updated the wiki (https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial) to make it more clear. Thank you for using Galaxy. M. On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar mailto:edgar.fernan...@umontreal.ca>> wrote: Hello Nicola and Martin,

Re: [galaxy-dev] errors installing tool dependencies...

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 ; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] e

Re: [galaxy-dev] errors installing tool dependencies...

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: January-25-16 11:11 AM To: 'Martin Čech' ; galaxy-...@bx.psu.e

Re: [galaxy-dev] errors installing tool dependencies...

-6111 poste 16568 From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola Soranzo Sent: January-25-16 12:22 PM To: Fernandez Edgar ; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] errors installing tool dependencies... Hi Edgar, indeed your bug was fixed lon

Re: [galaxy-dev] not sure what I can do about this...

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 (x86_64)

Re: [galaxy-dev] not sure what I can do about this...

: 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

Re: [galaxy-dev] not sure what I can do about this...

: 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: M

Re: [galaxy-dev] not sure what I can do about this...

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 2:29 PM To: Fernandez Edgar Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] not sure what I can do about this... Hi Fernandez, W

Re: [galaxy-dev] not sure what I can do about this...

es de 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 Cc: galaxy-...@bx.psu.edu S

Re: [galaxy-dev] not sure what I can do about this...

- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: May-26-16 3:32 AM To: Fernandez Edgar ; Nate Coraor Cc: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] not sure what I can do about this... Sorry Edgar, It looks like something else is causing this error (and my guess about different v

[galaxy-dev] delete user and all trace of user

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".

Re: [galaxy-dev] delete user and all trace of user

formation 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 ; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] delete user and all tr

[galaxy-dev] galaxy - bioperl - prokka

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 /usr/share/perl5/vend

Re: [galaxy-dev] galaxy - prokka - tbl2asn

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 ; galaxy-...@bx.psu.edu Subject: Re: [g

[galaxy-dev] galaxy - velvet devteam revision 08256557922f

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' rem

Re: [galaxy-dev] galaxy - velvet devteam revision 08256557922f

tréal 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 de

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

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 ; galaxy-...@bx.psu.edu Subject: RE: [galaxy-dev] new installation galaxy-17.05 - Unc

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

-6111 poste 16568 From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola Soranzo Sent: June 15, 2017 10:44 AM To: SAPET, Frederic ; Fernandez Edgar ; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error. Hi Edgar, Frederic, if you are

[galaxy-dev] galaxy config from 17.05 to 18.05

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 galaxy-17.05/c

Re: [galaxy-dev] galaxy config from 17.05 to 18.05

CustomLog /var/log/httpd/galaxy-prod-access_log common Please let me know what you guys think... Thank you, Edgar Fernandez Administrateur Système (Linux) Technologies de l'Information Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568 From: Fe