Very very slow response when a class is using Galaxy from a computer room in the university
Dear Sir/Madam, My Name is Ido Carmel, I am teaching the course titled "Advanced bioinformatics" in the Faculty of Agriculture in the Hebrew University (Israel). This year (around May), I used the Galaxy platform on the internet in a hands-on session about NGS data analysis. The session took place in one of the University computer classes with six students participating. For some reason, the Galaxy response was very very slow. It was slow when the students were signing up and also when the students were practicing very lightweight jobs that usually perform immediately such as "Fastq trimmer" or "fastq summary" statistics. Does the slow response was something seasonal or temporal? Alternatively, does the response is related to the fact that the students were in one computer room (and possibly all the queries were sent from the same proxy server)? I am teaching this course next year, do you have any advice/solution for me? Best Regards, Ido Carmel -- Ido Carmel, Dr. Yael Heifetz Lab, Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University, POB 12, Rechovot, Israel. Tel: (+)972-8-9489222
Dear Ido, The load on the Galaxy project public server ("main", aka usegalaxy.org) is often heavy and it's unpredictable when that will happen. As such teaching using main is not, um, recommended. About 18 months ago, the Galaxy project switched from using main for workshops to using cloud-based Galaxy instances. We use CloudMan to run and manage these servers on Amazon Web Services. This has gone much, much better, and I recommend you look into this option. Amazon has an education grants program that we are a part of and that I strongly recommend. See http://aws.amazon.com/grants/. It's not a lot of money, but if they award the grant it will likely be more than you need. And your question reminds me that I have been meaning to create wiki pages with best practices for running workshops and courses using Galaxy. If I get to that this week, I'll post an early draft page to this thread. Thanks, Dave C On Wed, Aug 21, 2013 at 4:39 AM, Ido Carmel <ido.carmel@mail.huji.ac.il>wrote:
Dear Sir/Madam,
My Name is Ido Carmel, I am teaching the course titled "Advanced bioinformatics" in the Faculty of Agriculture in the Hebrew University (Israel).
This year (around May), I used the Galaxy platform on the internet in a hands-on session about NGS data analysis. The session took place in one of the University computer classes with six students participating.
For some reason, the Galaxy response was very very slow. It was slow when the students were signing up and also when the students were practicing very lightweight jobs that usually perform immediately such as "Fastq trimmer" or "fastq summary" statistics.
Does the slow response was something seasonal or temporal? Alternatively, does the response is related to the fact that the students were in one computer room (and possibly all the queries were sent from the same proxy server)?
I am teaching this course next year, do you have any advice/solution for me?
Best Regards, Ido Carmel -- Ido Carmel, Dr. Yael Heifetz Lab, Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University, POB 12, Rechovot, Israel. Tel: (+)972-8-9489222
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Hello all, Thanks to Ido's post there is now a compute platforms for teaching page on the wiki: http://wiki.galaxyproject.org/Teach/ComputingPlatforms It currently has too much information, and also, not enough information. I'll keep massaging it through at least the end of this month and will send out a full announcement for it in the September Galaxy Update. In the meantime, suggestions and edits are welcome. Thanks, Dave C. On Wed, Aug 21, 2013 at 10:04 AM, Dave Clements <clements@galaxyproject.org>wrote:
Dear Ido,
The load on the Galaxy project public server ("main", aka usegalaxy.org) is often heavy and it's unpredictable when that will happen. As such teaching using main is not, um, recommended.
About 18 months ago, the Galaxy project switched from using main for workshops to using cloud-based Galaxy instances. We use CloudMan to run and manage these servers on Amazon Web Services. This has gone much, much better, and I recommend you look into this option.
Amazon has an education grants program that we are a part of and that I strongly recommend. See http://aws.amazon.com/grants/. It's not a lot of money, but if they award the grant it will likely be more than you need.
And your question reminds me that I have been meaning to create wiki pages with best practices for running workshops and courses using Galaxy. If I get to that this week, I'll post an early draft page to this thread.
Thanks,
Dave C
On Wed, Aug 21, 2013 at 4:39 AM, Ido Carmel <ido.carmel@mail.huji.ac.il>wrote:
Dear Sir/Madam,
My Name is Ido Carmel, I am teaching the course titled "Advanced bioinformatics" in the Faculty of Agriculture in the Hebrew University (Israel).
This year (around May), I used the Galaxy platform on the internet in a hands-on session about NGS data analysis. The session took place in one of the University computer classes with six students participating.
For some reason, the Galaxy response was very very slow. It was slow when the students were signing up and also when the students were practicing very lightweight jobs that usually perform immediately such as "Fastq trimmer" or "fastq summary" statistics.
Does the slow response was something seasonal or temporal? Alternatively, does the response is related to the fact that the students were in one computer room (and possibly all the queries were sent from the same proxy server)?
I am teaching this course next year, do you have any advice/solution for me?
Best Regards, Ido Carmel -- Ido Carmel, Dr. Yael Heifetz Lab, Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University, POB 12, Rechovot, Israel. Tel: (+)972-8-9489222
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/
-- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/
participants (2)
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Dave Clements -
Ido Carmel