cnv-seq running error

Question

[reza]

hi everyone i have a problem with running CNV-seq software in cygwin i have two files (as sample downloaded from http://tiger.dbs.nus.edu.sg/cnv-seq/) and try to run cnv-seq for first time but when enter this command:

$ ./cnv-seq.pl --test test.hits --ref ref.hits --genome chrom1 --log2 0.6 --p 0.001 --bigger-window 1.5 --annotate --minimum-windows 4

then i received below result and error:

genome size used for calculation is 247249719

test.hits: 1874797 reads

ref.hits: 1878852 reads

sh: R: command not found

 Error:
can not find program R at ./cnv-seq.pl line 117.

it should be note that i installed R software previously. where is the my mistake?

thanks in advance

[WouterDeCoster]

Is R in your $PATH? What do you get if you run (in a terminal) which R?

[reza]

it is my first time and this problem make me confuse,, how can i add R in my PATH?

i installed windows version of R, while cnv-seq wrote for linux, i use cygwin on windows. this can disrupt my analysis with cnv-seq?i must use cnv-seq on linux?

[WouterDeCoster]

I understand that you feel comfortable using Windows, but Linux is not as scary as you think. If you plan to do more bioinformatics, it's definitely worth to make the switch (e.g. to Ubuntu). You'll thank yourself later, your work will absolutely benefit from it. Many tools are exclusively for Linux and it's far more convenient for many tasks.

That said, if you want to keep your current setup, my guess would be that you need to install R in cygwin (although I've never used cygwin).

[reza]

thank you for your friendly advice