How To Install & Use R/Bioconductor In Amazon Ec2
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Entering edit mode
11.3 years ago

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 microarray cloud • 6.1k views
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Entering edit mode

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.

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

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

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11.3 years ago
User 6988 ▴ 70

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.

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

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11.3 years ago
Neilfws 49k

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).

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Entering edit mode
11.0 years ago

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

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