Differential intron excision analysis/leafcutter R package installation on Linux 64

[Aynur31]

Hello , I am performing differential splicing analysis on mouse RNA-Seq following this. I can not run leafcutter R installation step. IL6_BamFiles]$ ../scripts/leafcutter_ds.R --num_threads 4 leafcutter_perind_numers.counts.gz IL6_groups_file.txt -bash: ../scripts/leafcutter_ds.R: No such file or directory [akashgari19@login03 IL6_BamFiles]$ /kuacc/users/akashgari19/apps/leafcutter/scripts/leafcutter_ds.R --num_threads 4 leafcutter_perind_numers.counts.gz IL6_groups_file.txt Error in library(optparse) : there is no package called ‘optparse’ Execution halted I followed instructions to download leafcutter R package , but still could not solve this issue. Can you please help ? Thank you very much.

[jackhump]

If you read the error message it clearly says you don't have the optparse R package installed.

[Aynur31]

Thank you. I followed this link https://cran.r-project.org/web/packages/optparse/index.html to install the R package, but keeps giving me the same error.

[jackhump]

In an R session run library(optparse). If it gives an error then you need to install it with install.packages("optparse")

[Aynur31]

In an R session run library(optparse). If it gives an error then you need to install it with install.packages("optparse")

Sorry for the long comment. After installing optparse package, I still could not solve the issue, so I tried another way to install leafcutter R package. I used conda with the following command module load anaconda/3.6 source activate env_name conda install -c davidaknowles r-leafcutter I got it installed, then when I try to run the following command for DS, I again got an error message.

(env_name) [akashgari19@login03 IL6_BamFiles]$ /kuacc/users/akashgari19/leafcutter/scripts/leafcutter_ds.R --num_threads 4 leafcutter_perind_numers.counts IL6_groups_file.txt
Loading required package: Rcpp
Error: package or namespace load failed for ‘leafcutter’:
 package ‘leafcutter’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Execution halted`

In my conda env my R is version R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit).
I thought of changing R version, but I do not know what R version the leafcutter was installed with. 
Can you help me with this ? I am a biologist, new to this. Sorry for the trouble. 
Any advice is highly appreciated. 
Sincerely ,
Aynur.