[Useq-users] USeq installation problem w R

[Zeynep H. G. <zey...@gm...>]

Hi

I've installed USeq and also DESeq. When I open R in my local
directory, and library(DESeq), I see that it is there.
Now, when I try to run ChIPSeq, I get the following error:

mimi@panda TEST_MIMI $ java -Xmx2G -jar ../ChIPSeq -y sam -v
M_musculus_Jul_2007 -t ../../../MOUSE_SEQ/TRT_H3K4me/ -c
../../../MOUSE_SEQ/TRT_Input/ -r
/softlib/exe/x86_64/pkg/R/2.11.1/gcc_64/bin/R -s TEST

Checking parameters...
WARNING: ignoring environment value of R_HOME

The following problems were encountered when processing your parameter
file.  Correct and restart. ->

Error: Cannot find the required R library.  Did you install DESeq
(http://www-huber.embl.de/users/anders/DESeq/)?  See the author's
websites for installation instructions. Once installed, launch an R
terminal and type 'library(DESeq)' to see if it is present. Error
message:
                null

---
I am running it in a linux cluster, where R.11.1 is installed
globally. However, I install the libraries locally, such that my
.bashrc file is:

# to install R:
export R_HOME=/softlib/exe/x86_64/pkg/R/2.11.1/gcc_64
export PATH=$R_HOME/bin${PATH+:$PATH}
export R_LIBS=/panda_scratch_homes002/mimi/.R/mylibrary

How can I make ChIPSeq correctly? Is this a problem with my paths in
.bashrc (note that it works when I open R in the command line)?
ChIPSeq seems to go to the global network library as opposed to
mylibrary in my local folders.

Thank you for your help!
- Z