Commit 4ebabd72 authored by Spencer Barnes's avatar Spencer Barnes
Browse files

Merge branch '1-install-methylation' into 'master'

Resolve "Install methylation"

Closes #1

See merge request !1
parents 0d7d6b53 f669ef78
Pipeline #7209 failed with stages
in 25 minutes and 33 seconds
......@@ -270,8 +270,6 @@ process diffMeth{
module load R/3.5.1-gccmkl
module load python/3.6.1-2-anaconda
rm -rf ~/R
ls ~
R --version > version_r.txt
Rscript $baseDir/scripts/diff_meth.R -f $diffmethDesign -a $params.genome
"""
......
......@@ -3,9 +3,6 @@ Sys.setenv(https_proxy="proxy.swmed.edu:3128")
Sys.setenv(http_proxy="proxy.swmed.edu:3128")
chooseCRANmirror(ind=1)
dir.create("~/R")
dir.create("~/R/methylation_pipeline_libs")
.libPaths("~/R/methylation_pipeline_libs")
# Load libraries
install.packages("RCurl")
if (!requireNamespace("BiocManager", quietly = TRUE))
......@@ -35,13 +32,11 @@ if(!require("chromoMap")){
install.packages("chromoMap")
}
library(methylKit, lib.loc = "~/R/methylation_pipeline_libs")
library(argparse, lib.loc = "~/R/methylation_pipeline_libs")
library(htmltools, lib.loc = "~/R/methylation_pipeline_libs")
library(chromoMap, lib.loc = "~/R/methylation_pipeline_libs")
#source("/work/BICF/s181385/methylation_test_data/chromoMap.R")
library(methylKit)
library(argparse)
library(htmltools)
library(chromoMap)
#args <- commandArgs(TRUE)
# Create parser object
parser <- ArgumentParser()
......
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