Hello Boaz,
Galaxy itself will install and run in just a few minutes on most any laptop. And that install does include some very useful tools for basic usage (data manipulation, statistics, visualization). But you are correct - if you plan to do anything like NGS mapping followed by downstream analysis like ChIP-seq, RNA-seq, Variant Calling, etc. - then yes, you will need to give Galaxy access to sufficient resources to run those additional 3rd party tools. In general, those resources are the same as what you would need to provide anyway if you were running the same tools on the line-command.
Using a smaller reference genome may make you analysis project more manageable in scale, but there are other factors such as the size of the sequence files you intend to use as inputs and how many are used at a time (some tools permit the use of multiple samples with multiple replicates). How much throughput you want to achieve is also a consideration. Giving this a try by testing may be the best way to know if it is going to work for your particular needs.
Follow the set up instructions, then proceed to the advance configuration for setting up a production server. Install any necessary wrappers from the tool shed and dependencies for wrappers already in the distribution that you intend to use. And finally, install the data and indexes. All are documented and linked from the main 'Get Galaxy' wiki: http://getgalaxy.org
Many biologists find that using a cloud Galaxy is another alternative that helps them achieve more throughput, while avoiding having to deal with certain administration tasks or buying hardware, since the cloud image has many tools and core databases/indexes pre-installed and the dedicated resources can scaled up or down as needed. You can also add your own genome. Keeping a permanent or semi-permanent data storage bucket, but turning Galaxy "off" when not needed, is one way to manage costs. http://usegalaxy.org/cloud
You will also want to start following the galaxy-dev@bx.psu.edu mailing list, and begin asking local-install or cloud (if you go that route) questions there. http://wiki.galaxyproject.org/MailingLists#The_lists
Best,
Jen Galaxy team
On 6/3/13 11:42 PM, Boaz Shaanan wrote:
Hi,
I'd like to consider local install (linux) of Galaxy (pre-built binary or build from source). I was warned that analysis using Galaxy requires huge amount of memory (tens-Gb or even hundreds). I'm sure it's problem dependent though. For now I intend to do analysis vis-a-vis an archaeal genome, which is not too large. Is that practical to try to approach the problem on a recently purchased Quad-core computer with 8Gb memory or should I stick with the public implementation?
I'd appreciate your advice.
Boaz
/Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
E-mail: bshaanan@bgu.ac.il mailto:bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // /
/
*From:*galaxy-user-bounces@lists.bx.psu.edu mailto:galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] mailto:galaxy-user-bounces@lists.bx.psu.edu] on behalf of Dave Clements [clements@galaxyproject.org] mailto:clements@galaxyproject.org] *Sent:* Tuesday, June 04, 2013 12:35 AM *To:* Ramon Felciano *Cc:*galaxy-user@lists.bx.psu.edu mailto:galaxy-user@lists.bx.psu.edu *Subject:* Re: [galaxy-user] Newbie: summary or metrics of Galaxy use & adoption?
Hi Ramon,
The Galaxy Project does not track local installs directly. We don't even keep track of the number of times it is downloaded.
However, you can get an approximate feel for how widely used it is in a couple of other ways:
- Galaxy-Dev mailing list traffic and membership. Most messages to this list come from people doing local installs of Galaxy. There are a /lot/ of messages. http://wiki.galaxyproject.org/Galaxy%20Project/Statistics#Mailing_Lists
- Source code contributions from the community. See https://www.ohloh.net/p/galaxybx/
- The public Galaxy server list at http://wiki.galaxyproject.org/PublicGalaxyServers. These are all local installs (and this number may go up again this week).
- The isgalaxy tag in Galaxy's CiteUlike group. These papers are about installations of Galaxy. http://www.citeulike.org/group/16008/tag/isgalaxy
- The uselocal, usepublic, and uselocal tags at CiteULike. We started keeping track of these in March 2013. So this will give you an idea of how many papers since March indicate that the used a Galaxy other than Main.
We will be updating most of our statistics at the end of this month. We'll also be back-curating the new citeulike tags back to the beginning of 2013.
Hope this helps.
Dave C
On Thu, May 30, 2013 at 11:15 AM, Ramon Felciano <felciano@ingenuity.com mailto:felciano@ingenuity.com> wrote:
Hello all -- I would like to evaluate Galaxy for integration with Ingenuity's NGS analytics platform, and am trying to pull together some macro materials on how Galaxy has been used and adopted by the community at large. Are there any presentations or wiki pages that summarize basic stuff like: # users # of deployments/ instances (public or private) Relative use of CloudMan vs locally deployed Use in any clinical or regulated environments (e.g. CLIA) I've seen the materials at http://wiki.galaxyproject.org/Galaxy%20Project/Statistics but this looks to be only related to the public instance. Are there any similar materials that summarize across all installations, perhaps based on user surveys or the like? Thanks in advance for your help. Ramon ____________________________________ Ramon M. Felciano, PhD Founder and SVP, Research *INGENUITY*Systems, Inc. 1700 Seaport Blvd., 3rd Floor Redwood City, CA 94063 650.381.5100 phone 650.963.3399 fax E-mail: felciano@ingenuity.com <mailto:felciano@ingenuity.com> ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/-- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/
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: