Changeset 5807


Ignore:
Timestamp:
Jan 10, 2020, 8:18:28 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1215: Include mutation signature analysis in the variant calling pipeline

Added a wrapper shell script for starting R scripts with R 3.6.2. We need to set PATH and LD_LIBRARY_PATH so that R can find the correct versions.

Location:
other/pipeline/trunk
Files:
1 added
1 edited

Legend:

Unmodified
Added
Removed

  • other/pipeline/trunk/mutation_signature.R

    r5796 r5807  
    11#!/usr/bin/env Rscript
    22
    3 ## TODO - since we need a specific R version the path above should probably be changed
    4 ## to /usr/local/packages/R/3.6.2/bin/Rscript
     3## NOTE! Since we need a specific R version (3.6.2) this script need
     4## to be started via the Rscript.sh wrapper.
    55#
    66# $Id$
    … …  
    5252## read vcf
    5353vcfs <- read_vcfs_as_granges(vcfPath, sampleName, ref_genome)
    54 
    55 str(vcfs)
    5654
    5755## extract mutations
Note: See TracChangeset for help on using the changeset viewer.