Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor.
Thank you
Julie
Hi Julie, All,
I have a similar problem on a test environment with a postgres backend. The file that I'm uploading is a 50MB GTF file and it I'm getting the same behavior. Any help would be appreciated.
Thanks,
Jason
-- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum@liai.org La Jolla Institute for Allergy and Immunology
----- Original Message -----
From: "julie dubois" dubjulie@gmail.com To: galaxy-dev@lists.bx.psu.edu Sent: Tuesday, May 22, 2012 12:12:06 AM Subject: [galaxy-dev] Uploading problem
Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor.
Thank you
Julie
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Are these problems cropping up because of possible system resource limits being imposed on the user that is running galaxy? It may be worthwhile to check the /etc/login.conf (not sure that the analogous file is in Ubuntu). Same may be true for Postgres (http://www.postgresql.org/docs/8.2/static/kernel-resources.html).
--hk
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of J. Greenbaum Sent: Tuesday, May 22, 2012 9:50 AM To: julie dubois Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Uploading problem
Hi Julie, All,
I have a similar problem on a test environment with a postgres backend. The file that I'm uploading is a 50MB GTF file and it I'm getting the same behavior. Any help would be appreciated.
Thanks,
Jason
-- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum@liai.orgmailto:jgbaum@liai.org La Jolla Institute for Allergy and Immunology
________________________________ From: "julie dubois" <dubjulie@gmail.commailto:dubjulie@gmail.com> To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Sent: Tuesday, May 22, 2012 12:12:06 AM Subject: [galaxy-dev] Uploading problem
Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor.
Thank you
Julie
___________________________________________________________ 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:
Thanks for your answer. I've solved the problem in another way : I've used Upload files from filesystem paths. It's very quick because it doesn't upload the files, just save the path where the data is!
Thanks Julie
2012/5/22 Kelkar, Hemant hkelkar@unc.edu
Are these problems cropping up because of possible system resource limits being imposed on the user that is running galaxy? ****
It may be worthwhile to check the /etc/login.conf (not sure that the analogous file is in Ubuntu). Same may be true for Postgres ( http://www.postgresql.org/docs/8.2/static/kernel-resources.html).****
--hk****
*From:* galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edu] *On Behalf Of *J. Greenbaum *Sent:* Tuesday, May 22, 2012 9:50 AM *To:* julie dubois *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Uploading problem****
Hi Julie, All,****
I have a similar problem on a test environment with a postgres backend. The file that I'm uploading is a 50MB GTF file and it I'm getting the same behavior. Any help would be appreciated.****
Thanks,****
Jason****
--****
*Jason Greenbaum, Ph.D. *Manager, Bioinformatics Core | jgbaum@liai.org La Jolla Institute for Allergy and Immunology****
*From: *"julie dubois" dubjulie@gmail.com *To: *galaxy-dev@lists.bx.psu.edu *Sent: *Tuesday, May 22, 2012 12:12:06 AM *Subject: *[galaxy-dev] Uploading problem
Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor.
Thank you
Julie
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:
Hi,
Hanging uploads have been a problem before with small and large files: http://comments.gmane.org/gmane.science.biology.galaxy.devel/4583
I don't know if it's been fixed, but it seemed to depend on browser choice and on what server was running. I was recommended to use the nginx server IIRC. I still have the occasional problem though, but (I hope) less often.
cheers, jorrit
On 05/22/2012 03:50 PM, J. Greenbaum wrote:
Hi Julie, All,
I have a similar problem on a test environment with a postgres backend. The file that I'm uploading is a 50MB GTF file and it I'm getting the same behavior. Any help would be appreciated.
Thanks,
Jason
-- *Jason Greenbaum, Ph.D. *Manager, Bioinformatics Core | jgbaum@liai.org mailto:jgbaum@liai.org La Jolla Institute for Allergy and Immunology
*From: *"julie dubois" <dubjulie@gmail.com> *To: *galaxy-dev@lists.bx.psu.edu *Sent: *Tuesday, May 22, 2012 12:12:06 AM *Subject: *[galaxy-dev] Uploading problem Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor. Thank you Julie ___________________________________________________________ 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: http://lists.bx.psu.edu/
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:
Thanks for the info. It's definitely browser-related as I was having the issue in Chrome, but FF seems to be working...
-J
-- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgbaum@liai.org La Jolla Institute for Allergy and Immunology
----- Original Message -----
From: "Jorrit Boekel" jorrit.boekel@scilifelab.se To: "J. Greenbaum" jgbaum@liai.org, galaxy-dev@lists.bx.psu.edu Sent: Tuesday, May 22, 2012 7:04:26 AM Subject: Re: [galaxy-dev] Uploading problem
Hi,
Hanging uploads have been a problem before with small and large files: http://comments.gmane.org/gmane.science.biology.galaxy.devel/4583
I don't know if it's been fixed, but it seemed to depend on browser choice and on what server was running. I was recommended to use the nginx server IIRC. I still have the occasional problem though, but (I hope) less often.
cheers, jorrit
On 05/22/2012 03:50 PM, J. Greenbaum wrote:
Hi Julie, All,
I have a similar problem on a test environment with a postgres backend. The file that I'm uploading is a 50MB GTF file and it I'm getting the same behavior. Any help would be appreciated.
Thanks,
Jason
-- Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgbaum@liai.org
La Jolla Institute for Allergy and Immunology
----- Original Message -----
From: "julie dubois" dubjulie@gmail.com
To: galaxy-dev@lists.bx.psu.edu
Sent: Tuesday, May 22, 2012 12:12:06 AM
Subject: [galaxy-dev] Uploading problem
Hi,
I test a production environnement of Galaxy with apache proxy and mysql database.
It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish!
Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor.
Thank you
Julie
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:
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: http://lists.bx.psu.edu/
galaxy-dev@lists.galaxyproject.org
-
J. Greenbaum -
Jorrit Boekel -
julie dubois -
Kelkar, Hemant