snakemake r script

Question

[nishimalhotra2612]

hi all

i have been trying to execute r script of variant call analysis in a snakemake

rule VCA analysis:

shell:
    "Rscript vca.R"

but when i run it, but it gives the error

Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning in install.packages("BiocManager") : 'lib = "/usr/local/lib/R/site-library"' is not writable Error in install.packages("BiocManager") : unable to install packages Execution halted

why is it showing this kind of error ??

[ATpoint]

Consider to install required software first, either locally, conda or via Docker/Singularity. Installing software as part of a pipeline is suboptimal, as it can throw errors that need to be addressed manually.

[nishimalhotra2612]

thanks i will modify script and will install the needed package

Answer 1

[Mensur Dlakic]

'lib = "/usr/local/lib/R/site-library"' is not writable

It would appear that you don't have administrator privileges, because that's what is required to install anything in /usr/local/lib directory. Maybe it will work if you install ahead of time the needed packages from that script you are trying to run (or ask someone to do it for you), and then comment out the installation lines.

[nishimalhotra2612]

thank you so much