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 [email protected] 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: [email protected] <mailto:[email protected]>
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710 /
//
//
/
/
------------------------------------------------------------------------
*From:*[email protected]
<mailto:[email protected]>
[[email protected]]
<mailto:[email protected]]> on behalf of Dave
Clements [[email protected]] <mailto:[email protected]]>
*Sent:* Tuesday, June 04, 2013 12:35 AM
*To:* Ramon Felciano
*Cc:*[email protected] <mailto:[email protected]>
*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
<[email protected] <mailto:[email protected]>> 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: [email protected] <mailto:[email protected]>
___________________________________________________________
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
