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EcholocatoR.md

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EcholocatoR package installation on Alpine:

According to the bioconductor page, EcholocatoR is "An Automated statistical and functional fine-mapping with extensive access to genome-wide datasets.". To reference this package, please cite:

Brian M Schilder, Jack Humphrey, Towfique Raj (2021) echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline, Bioinformatics; btab658, https://doi.org/10.1093/bioinformatics/btab658

Below are the following steps in order to install EcholocatoR on Alpine:

EcholocatoR package installation steps.

  1. Step 1: Create a token

The first thing to do is for you to create a token, because otherwise you will exhaust the Github API rate limit which is set at 60 requests per hour.

  1. Step 2: Resource Allocation:
module load slurm/alpine 
acompile --ntasks=2 --time=01:30:00
  1. Step 3: Load the appropriate modules and dependencies:

Here we load the appropriate gcc compiler along with gsl jpeg and R in one line.

ml gcc gsl jpeg R
  1. Step 4: Prepare the appropriate paths & environment files
  • We create the directory containing echolocatoR inside /projects/$USER
  • We cd to it
  • We create a local directory where you will install r-packages.
  • We create the R environment file where you will be able to specify important paths
mkdir /projects/$USER/software/echolochatoR 
cd /projects/$USER/software/echolochatoR 
mkdir r-packages 
touch .Renviron
  1. Step 5: Editing the .Renviron file. In the .R environ file, please add the following paths: (Note: remember to change $USER with your actual username).
R_LIBS_USER=/projects/$USER/software/echolochatoR/r-packages:/curc/sw/install/jpeg/9d/gcc/11.2.0/lib:/projects/$USER/software/echolochatoR/r-packages:/curc/sw/install/R/4.2.2/lib64:/curc/sw/jdk/18.0.1.1/lib:/curc/sw/install/R/4.2.2/lib64/R/lib:/usr/lib:/usr/lib64:/projects/$USER/software/R_libs/4.2:/curc/sw/install/gsl/2.7/gcc/11.2.0/lib:/projects/$USER/software/echolochatoR/lib 
 
R_INCLUDE_DIR=/curc/sw/install/R/4.2.2/lib64/R/include:/curc/sw/install/jpeg/9d/gcc/11.2.0/include:/usr/include:/usr/include/freetype2:/curc/sw/install/gsl/2.7/gcc/11.2.0/include 
 
CPATH=/curc/sw/install/jpeg/9d/gcc/11.2.0/include:/usr/local/include:/usr/include:/usr/include/freetype2:/curc/sw/install/R/4.2.2/lib64/R/include:/curc/sw/install/gsl/2.7/gcc/11.2.0/include 
 
PKG_CONFIG_PATH=/curc/sw/install/gcc/11.2.0/lib64/pkgconfig:/curc/sw/install/gsl/2.7/gcc/11.2.0/lib/pkgconfig:/usr/local/lib/pkgconfig:/curc/sw/install/jpeg/9d/gcc/11.2.0/lib/pkgconfig/ 
LD_LIBRARY_PATH=/curc/sw/install/R/4.2.2/lib64:/curc/sw/install/jpeg/9d/gcc/11.2.0/lib:/curc/sw/jdk/18.0.1.1/lib:/curc/sw/install/gsl/2.7/gcc/11.2.0/lib:/curc/sw/install/gcc/11.2.0/lib64 
 
LIBRARY_PATH=/curc/sw/install/R/4.2.2/lib64:/curc/sw/install/jpeg/9d/gcc/11.2.0/lib:/curc/sw/jdk/18.0.1.1/lib:/curc/sw/install/gsl/2.7/gcc/11.2.0/lib:/curc/sw/install/gcc/11.2.0/lib64
  1. Step 6: Package installation
  • Launch R by typing R.
  • Install the EcholocatoR package by copying and pasting the lines below. Note: Make sure to replace "YOUR_PAT_Token" by your actual PAT token.
credentials::set_github_pat("YOUR_PAT_Token") 
if(!require("remotes")) install.packages("remotes") 
remotes::install_github("RajLabMSSM/echolocatoR") 
library(echolocatoR)