Commit f08f5cfa authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Resolve memrge.

parents a1b06250 0d7d6b53
......@@ -26,7 +26,7 @@ process {
}
withName: diffMeth{
module = ['R/3.6.1-gccmkl', 'python/3.6.1-2-anaconda']
module = ['R/3.5.1-gccmkl', 'python/3.6.1-2-anaconda']
queue = '128GB,256GB,256GBv1'
//queue = 'super'
}
......
......@@ -24,10 +24,13 @@ process trackStart {
curl -H 'Content-Type: application/json' -X PUT -d \
'{ \
"sessionId": "${workflow.sessionId}", \
"pipeline": "astrocyte.methylation_analysis", \
"pipeline": "methylation_analysis", \
"start": "${workflow.start}", \
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}", \
"astrocyte": false, \
"ci": false, \
"dev": false \
}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
......@@ -264,7 +267,7 @@ process diffMeth{
script:
"""
module load R/3.6.1-gccmkl
module load R/3.5.1-gccmkl
module load python/3.6.1-2-anaconda
rm -rf ~/R
......
......@@ -4,9 +4,19 @@ Sys.setenv(http_proxy="proxy.swmed.edu:3128")
chooseCRANmirror(ind=1)
# Load libraries
install.packages("RCurl")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicRanges")
BiocManager::install("GenomeInfoDb")
BiocManager::install("Rsamtools")
BiocManager::install("fastseq")
BiocManager::install("rtracklayer")
if(!require("methylKit")){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
BiocManager::install("methylKit")
}
......@@ -22,10 +32,18 @@ if(!require("chromoMap")){
install.packages("chromoMap")
}
<<<<<<< HEAD
library(methylKit)
library(argparse)
library(htmltools)
library(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")
>>>>>>> master
# Create parser object
......
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