Arup Ghosh arupgsh

Install OmicVerse with all dependencies

The conda environment was tested in following settings.

OS: WSL2/Ubuntu 24.04.2 CUDA: 12.3

The repository for the assignment is public and Github does not allow the creation of private forks for public repositories.

The correct way of creating a private frok by duplicating the repo is documented here.

For this assignment the commands are:

Create a bare clone of the repository. (This is temporary and will be removed so just do it wherever.)

git clone --bare [email protected]:usi-systems/easytrace.git

ssh-keygen.exe

	library(dplyr)
	library(forcats)
	library(ggplot2)
	library(palmerpenguins)
	library(ggtext)
	library(colorspace)
	library(ragg)

	url <- "https://raw.githubusercontent.com/allisonhorst/palmerpenguins/master/man/figures/lter_penguins.png"
	img <- magick::image_read((url))

	# Source: https://stackoverflow.com/a/43317244
	$path = ".\aws-ec2-key.pem"
	# Reset to remove explict permissions
	icacls.exe $path /reset
	# Give current user explicit read-permission
	icacls.exe $path /GRANT:R "$($env:USERNAME):(R)"
	# Disable inheritance and remove inherited permissions
	icacls.exe $path /inheritance:r

	*bcftools filter
	*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
	qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

	*printing out info for only 2 samples:
	bcftools view -s NA20818,NA20819 filename.vcf.gz

	*printing stats only for variants passing the filter:
	bcftools view -f PASS filename.vcf.gz

	#!/bin/bash

	# exit when any command fails
	set -e

	#get start time for calculating time taken to complete the process
	start=$(date +%s)

	#source location, backup location and archive names
	SRCDIR="/var/www/html/"

	# Last update 27-10-2021
	# network scheme was create using https://netplan.io/reference/
	# The following configuration assumes the first interface has internet access
	# CIDR calculator https://mxtoolbox.com/subnetcalculator.aspx
	network:
	ethernets:
	eno1:
	addresses:
	- xxx.xxx.xxx.xxx/24 #IPV4 address for interface 1
	routes:

	## If you are facing timeout [Error 12] with official repository
	## Check the commans before running as root

	#sudo yum remove docker docker-client docker-client-latest docker-common docker-latest docker-latest-logrotate docker-logrotate docker-engine # remove previous version

	sudo yum install -y yum-utils

	sudo yum-config-manager --add-repo http://mirrors.aliyun.com/docker-ce/linux/centos/docker-ce.repo

	#yum list docker-ce --showduplicates \| sort -r #List all available docker versions

	#!/bin/bash

	###################################################################
	#Script Name : Nanoclust Demo
	#Description : NanoCLUST installation test for Centos 7
	#Author : Arup Ghosh
	#Web : https://arup.dev
	###################################################################

	set -e