NGSrich target enrichment: software error

Question

[NB]

Hi,

Has anyone tried running the NGSrich software ?

I am trying to run

cd /software/NGSrich_0.7.8/bin
java NGSrich evaluate \
-r sample.bam \
-u hg19 \
-t /target_genes.bed \
-a refGene.txt \
-T /scratch/tmp  \
-o /NGSrich /coverage

and I get an error saying

======================0======================
STEP 0: Checking and Validation Step
Checking Requirements: Rscript is not on your PATH.
======================0======================

I tried exported the path with the Rscripts but the error still persists.

export PATH=$PATH:/software/NGSrich_0.7.8/R

Any idea where I may be going wrong ?

Many thanks,

Answer 1

[User 59]

Rscript in this instance is probably not in the "R scripts" directory of NGSrich, as is is a separate entity: http://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html and is used for running R scripts at the terminal. Make sure your $PATH includes that directory.