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Install OmicVerse with all dependencies

Requirements:

The conda environment was tested in following settings.

OS: WSL2/Ubuntu 24.04.2 CUDA: 12.3

CUDA installation (WSL 2)

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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:

1. 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

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# 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

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*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

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#!/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/"

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Passwordless ssh from PowerShell

Source: https://www.chrisjhart.com/Windows-10-ssh-copy-id/

• Generate SSH Key

ssh-keygen.exe 

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# 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:

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## 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

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#!/bin/bash

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

set -e

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#!/usr/bin/python3 env
# -*- coding: utf-8 -*-

"""Qsub command generator
    Author: Arup Ghosh 
    Creation date: 17/07/2019
    last modified: 18/07/2019
    Email: email [at] gmail.com
"""
import glob