Set up environment & install software

Run these commands in the root directory of this package

1. Make the following directories for output & temp file writing (data & imputations) and storage of imputation software (tools). done folder for finished imputation symlinks.

mkdir data
mkdir tools
mkdir done
mkdir imputations

2. Install fundamental packages & R

VAR=$PWD
export VAR
sudo apt-get update
sudo apt-get install r-base-dev
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install default-jdk
sudo apt-get install dos2unix

Use sudo yum install <package> on other Linux distributions.

3. Install R-packages

sudo -i
R
if (!requireNamespace("BiocManager"))
  install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c('Mega2R'))
install.packages("rmarkdown")
install.packages("openxlsx")
install.packages("nlme")
install.packages("R.utils")
install.packages("mailR")
install.packages("rJava")
install.packages("tools")
install.packages("httr")
install.packages("aws.s3")
q()
y
exit

4. Install git

sudo apt-get install git

5. Download and unpack imputation related software. Confirm that the version is appropriate for the OS of the server.

Impute2

cd tools
wget https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_static.tgz
gunzip impute_v2.3.2_x86_64_static.tgz
tar -xvf impute_v2.3.2_x86_64_static.tar
mv imput* Impute2
cd $VAR

ShapeIt

cd tools
wget https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.static.tgz
tar zxvf shapeit.v2.r837.GLIBCv2.12.Linux.static.tgz
mv shapei* Shapeit
cd $VAR

Gtool

cd tools
mkdir Gtool
cd Gtool
wget http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool_v0.7.5_x86_64.tgz
tar zxvf gtool_v0.7.5_x86_64.tgz
mv gtoo* gtool
cd $VAR

Plink

cd tools
wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20181202.zip
unzip plink_linux_x86_64_20181202.zip
mv plink* Plink
cd $VAR

6. I have already downloaded and preprocessed all reference data. It is located in the 'ref' directory.

'ref' directory to be uploaded...

7. Edit config file for cron job. Imputation is setup to run as a cron job so that it is automated. Parameters for the cron job are given in the file 'misc_files/config.r'.

8. Setup a cron job so imputation is performed every hour (you can change this to occur more or less frequently). Imputation is only performed on files that have been processed after upload.

crontab -e 
50 * * * * cd ImputationGeneris && /home/ec2-user/R-3.5.2/bin/Rscript scripts/imputation_cron_job.R > logs/cron_logs/`date +\%Y\%m\%d\%H\%M\%S`-impute-cron.log 2>&1

9. Link file upload to the script 'step1.sh'. This script runs an R script that preprocesses raw DNA data file from 23andme, Ancestry DNA, or My Heritage.

./step1.sh