Question: How To Install & Use R/Bioconductor In Amazon Ec2
3
gravatar for Carlos Villacorta
9.3 years ago by
Carlos Villacorta250 wrote:

I'd like to explore and analyze arrays in the cloud using Bioconducor and EC2.

I found this instructions. I launched an Amazon microinstance (free usage tier), logged in and followed the instructions:


wget http://cran.at.r-project.org/src/base/R-2/R-2.12.1.tar.gz
tar xf R-2.12.1.tar.gz
cd R-2.12.1
sudo yum install gcc
yum install gcc-c++
yum install gcc-gfortran
yum install readline-devel
./configure            ## returns error
./configure --with-x=no    ## configure with something missing?
make
PATH=$PATH:~/R-2.12.1/bin/
R                ## seems to work ok

Looks like the same problem as the r-blogger above. I wonder:

  • What is causing that error.
  • What's the limitation of configuring it with -x=no versus the right way?

Also I'd like to make a list of reliable, bioinformatics-oriented public instances (AMIs). Grossman has an AMI with R installed already. Venter's JCVI Cloud Bio-Linux looks quite comprehensive. (I've seen interesting resources in this BioStar thread). Any other suggestions?

I appreciate general advice for running occasional heavy analyses in EC2. Many thanks,

R cloud microarray • 5.4k views
ADD COMMENTlink modified 9.3 years ago by Daniel Fuentes10 • written 9.3 years ago by Carlos Villacorta250

did you first try to install the normal and recommended way via the yum manager? If that does not work maybe you could start a different type of unix instance.

ADD REPLYlink written 9.3 years ago by Istvan Albert ♦♦ 84k

probably mndoci will give you best way to achieve this task!

ADD REPLYlink written 9.3 years ago by Thaman3.2k

Someone already beat me to it, and I wasn't even aware :)

ADD REPLYlink written 9.3 years ago by Mndoci1.2k
7
gravatar for User 6988
9.3 years ago by
User 698870
User 698870 wrote:

Also, Bioconductor is releasing its own AMI, preconfigured with R, X11, and many Bioconductor packages.

The link is here.

This AMI uses R-2.13, which is not yet officially released, and the AMI itself should be considered beta, but it will be officially released along with Bioconductor 2.8 on or around April 14th, 2011. It is, however, available for use now.

Any feedback you'd like to give on the AMI would be welcomed.

ADD COMMENTlink modified 10 months ago by RamRS27k • written 9.3 years ago by User 698870

awesome! thanks, I'll definitely give it a try

ADD REPLYlink written 9.3 years ago by Carlos Villacorta250
2
gravatar for Neilfws
9.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Configuring --with-x=no means that X11 window support is not compiled into R. X11 is the default graphical option so when you type, for example, plot(x), the plot will not open in a window.

To configure with X11, you need to install the required libraries and headers. There is most likely a package named something like libx11 and ending with -devel or -dev that you can install using yum. On Ubuntu, which is a little different, it's called libx11-dev.

The general rule when configure fails is to look at the error message, then try to find a development package corresponding to the error. For example, if you see png, you probably need something like libpng12-dev.

Having said all that, it's a lot easier to install R itself from the package manager. If you need the latest version (currently 2.12), you can add a CRAN repository to your yum configuration directory, /etc/yum.repos.d/. See this article for instructions. Note that the base URL will have changed since the article was written; you want something like cran.ms.unimelb.edu.au/bin/linux/redhat/fedora11/. Choose a mirror site close to you (that URL is an Australian example, which I use).

ADD COMMENTlink modified 10 months ago by RamRS27k • written 9.3 years ago by Neilfws48k
1
gravatar for Daniel Fuentes
9.0 years ago by
Daniel Fuentes10 wrote:

My beta account on cloudnumbers.com (they actually provide R in the cloud) was unlocked yesterday, and what i've seen so far is looks pretty good. maybe you should give it a try as well, as it seems very easy to use

ADD COMMENTlink written 9.0 years ago by Daniel Fuentes10
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