Break through the practice of writing tedious code with shell scriptsAbout This BookLearn to impeccably build shell scripts and develop advanced applicationsCreate smart solutions by writing and ...debugging scriptsA step-by-step tutorial to automate routine tasks by developing scriptsWho This Book Is ForLearning Linux Shell Scripting is ideal for those who are proficient at working with Linux and want to learn about shell scripting to improve their efficiency and practical skills.What You Will LearnFamiliarize yourself with the various text filtering tools available in LinuxUnderstand expressions and variables and how to use them practicallyAutomate decision-making and save a lot of time and effort of revisiting codeGet to grips with advanced functionality such as using traps, dialogs to develop screens & Database administration such as MySQL or OracleStart up a system and customize a Linux systemTaking backup of local or remote data or important files.Use existing other language scripts such as Python, Perl & Ruby in Shell ScriptsIn DetailLinux is the most powerful and universally adopted OS. Shell is a program that gives the user direct interaction with the operating system. Scripts are collections of commands that are stored in a file. The shell reads this file and acts on commands as if they were typed on the keyboard.Learning Linux Shell Scripting covers Bash, GNU Bourne Again Shell, preparing you to work in the exciting world of Linux shell scripting. CentOS is a popular rpm-based stable and secured Linux distribution. Therefore, we have used CentOS distribution instead of Ubuntu distribution. Linux Shell Scripting is independent of Linux distributions, but we have covered both types of distros. We start with an introduction to the Shell environment and basic commands used. Next, we explore process management in Linux OS, real-world essentials such as debugging and perform Shell arithmetic fluently. You'll then take a step ahead and learn new and advanced topics in Shell scripting, such as decision making, starting up a system, and customizing a Linux environment. You will also learn about grep, stream editor, and AWK, which are very powerful text filters and editors. Finally, you'll get to grips with taking backup, using other language scripts in Shell Scripts as well as automating database administration tasks for MySQL and Oracle.By the end of this book, you will be able to confidently use your own shell scripts in the real world.Style and approachThis practical book will go from the very basics of shell scripting to complex, customized automation. The idea behind this book is to be as practical as possible and give you the look and feel of what real-world scripting is like.
Practical and actionable recipes for using shell and command-line scripting on your Linux OS with confidenceKey FeaturesLearn how to use the command line and write and debug Linux Shell ...scriptsAutomate complex repetitive tasks and backups, and learn networking and securityA practical approach to system administration, and virtual machine and software managementBook DescriptionLinux Command Line and Shell Scripting Techniques begins by taking you through the basics of the shell and command-line utilities. You'll start by exploring shell commands for file, directory, service, package, and process management. Next, you'll learn about networking - network, firewall and DNS client configuration, ssh, scp, rsync, and vsftpd, as well as some network troubleshooting tools.You'll also focus on using the command line to find and manipulate text content, via commands such as cut, egrep, and sed. As you progress, you'll learn how to use shell scripting. You'll understand the basics - input and output, along with various programming concepts such as loops, variables, arguments, functions, and arrays. Later, you'll learn about shell script interaction and troubleshooting, before covering a wide range of examples of complete shell scripts, varying from network and firewall configuration, through to backup and concepts for creating live environments. This includes examples of performing scripted virtual machine installation and administration, LAMP (Linux, Apache, MySQL, PHP) stack provisioning and bulk user creation for testing environments. By the end of this Linux book, you'll have gained the knowledge and confidence you need to use shell and command-line scripts.What you will learnGet an introduction to the command line, text editors, and shell scriptingFocus on regular expressions, file handling, and automating complex tasksAutomate common administrative tasksBecome well-versed with networking and system security scriptingGet to grips with repository management and network-based file synchronizationUse loops, arguments, functions, and arrays for task automationWho this book is forThis book is for anyone looking to learn about Linux administration via CLI and scripting. Those with no Linux command-line interface (CLI) experience will benefit from it by learning from scratch. More experienced Linux administrators or engineers will also find this book useful, as it will help them organize their knowledge, fill in any gaps, and work efficiently with shell scripts to increase productivity.
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract ...biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/ ) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.
From the bash shell to the traditional UNIX programs, and from redirection and pipes to automating tasks, Command Line Fundamentals teaches you all you need to know about how command lines work.
MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art ...programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.
Population genetic analyses often use summary statistics to describe patterns of genetic variation and provide insight into evolutionary processes. Among the most fundamental of these summary ...statistics are π and dXY, which are used to describe genetic diversity within and between populations, respectively. Here, we address a widespread issue in π and dXY calculation: systematic bias generated by missing data of various types. Many popular methods for calculating π and dXY operate on data encoded in the variant call format (VCF), which condenses genetic data by omitting invariant sites. When calculating π and dXY using a VCF, it is often implicitly assumed that missing genotypes (including those at sites not represented in the VCF) are homozygous for the reference allele. Here, we show how this assumption can result in substantial downward bias in estimates of π and dXY that is directly proportional to the amount of missing data. We discuss the pervasive nature and importance of this problem in population genetics, and introduce a user‐friendly UNIX command line utility, pixy, that solves this problem via an algorithm that generates unbiased estimates of π and dXY in the face of missing data. We compare pixy to existing methods using both simulated and empirical data, and show that pixy alone produces unbiased estimates of π and dXY regardless of the form or amount of missing data. In summary, our software solves a long‐standing problem in applied population genetics and highlights the importance of properly accounting for missing data in population genetic analyses.
The goal of fine-mapping in genomic regions associated with complex diseases and traits is to identify causal variants that point to molecular mechanisms behind the associations. Recent fine-mapping ...methods using summary data from genome-wide association studies rely on exhaustive search through all possible causal configurations, which is computationally expensive.
We introduce FINEMAP, a software package to efficiently explore a set of the most important causal configurations of the region via a shotgun stochastic search algorithm. We show that FINEMAP produces accurate results in a fraction of processing time of existing approaches and is therefore a promising tool for analyzing growing amounts of data produced in genome-wide association studies and emerging sequencing projects.
FINEMAP v1.0 is freely available for Mac OS X and Linux at http://www.christianbenner.com
: christian.benner@helsinki.fi or matti.pirinen@helsinki.fi.
The goal of this book is to introduce readers to three powerful command line utilities that can be combined to create simple yet powerful shell scripts for performing a multitude of tasks. --
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