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Command line in MS-DOS begins with a machine-generated prompt and then is implied to be filled with symbols and words which altogether must be suitable for machine interpretation according to certain syntax conventions. The final ENTER keystroke initializes interpretation of command line by a resident program — the command interpreter. Implementation of syntax conventions by different interpreters is not just the same.
MS-DOS 7 provides 3 interpreters: IO.SYS, COMMAND.COM, and DEBUG.EXE. Each interpreter accepts its own set of commands.
1 Named objects and their names
1.1 Reserved words
1.2 Names and suffixes
1.3 Filemasks and wildcards
2.1 Typical path structure
2.2 The PATH variable
2.3 Dot(s) in path specifications
3 Tips on command line parsing syntax
3.1 Separation symbols
3.2 A slash
3.3 Percent sign
3.4 Double quote sign ( " )
3.5 Square brackets
4 Syntactic marks with command mission
4.2 Left Arrow
4.3 Right Arrow
4.4 Double Right Arrow
4.5 Vertical bar (or "pipe")
4.6 The "at" ( @ ) sign
Command Line Essentials for Bioinformaticians
Training course for BCC2020
We will start the session with a quick refresher on the basics of bash. I will then introduce a few well known unix tools and features of the shell with a focus on how to use these to make key bioinformatics tasks easier and more efficient.
As bioinformaticians we regularly deal with directories filled with hundreds of files and have to manage running an equally large number of parallel jobs. There are many features of the shell that can make this easier. Here I will focus on some of the key ones that I use often. Tools: bash (loops, functions, strings), xargs, parallel
Lots of bioinformatics data is tabular, gff, vcf, sam. Using these formats as examples I will introduce some useful tools for manipulating tabular data Tools: cut, paste, awk, shuff, comm
Manipulating sequence data like fasta and fastq requires specialised bioinformatic tools. Two very useful ones are samtools and bioawk. This section will show you how to easily accomplish common tasks like splitting, sampling or reformatting a large sequence file. Tools: samtools, bioawk
A laptop with a modern web browser
Command line tool for machine learning on AWS awstrainer helps you run machine learning tasks (or any other long-running computations) on AWS. With one simple command, it spins up an AWS instance (from your own account), transfers your code & dataset, starts the training run, syncs all output files back to your computer, and terminates the instance after training has finished. It really shines when you need to quickly launch multiple, long-running jobs in parallel (e.g. for hyperparameter optimization).
A command line interface (CLI) language phrase training program written in Python.
PhraseTrain | Test P - Practice the chosen list M - Modify the current list S - Save the current list R - Remove the current list L - Load a previous phrase list C - Create a new phrase list Q - Quit the program What would you like to do? Choice >> m
PhraseTrain | Modify 'Test' (English -> Russian)
PhraseTrain | Setup practice for 'Test' (English -> Russian)
websocketd is a small command-line tool that will wrap an existing command-line interface program, and allow it to be accessed via a WebSocket. WebSocket-capable applications can now be built very easily. As long as you can write an executable program that reads
STDIN and writes to
STDOUT, you can build a WebSocket server. Do it in Python, Ruby, Perl, Bash, .NET, C, Go, PHP, Java, Clojure, Scala, Groovy, Expect, Awk, VBScript, Haskell, Lua, R, whatever! No networking libraries necessary. Details Upon startup,
websocketd will start a WebSocket server on a specified port, and listen for connections. Upon a connection, it will fork the appropriate process, and disconnect the process when the WebSocket connection closes (and vice-versa). Any message sent from the WebSocket client will be piped to the process's
STDIN stream, followed by a
\n newline. Any text printed by the process to
STDOUT shall be sent as a WebSocket message whenever a
\n newline is encountered.
SensioLabs Security Checker
The SensioLabs Security Checker is a command line tool that checks if your application uses dependencies with known security vulnerabilities. It uses the TIP: As an alternative, you can use the [Symfony CLI] tool that has the following advantages: it does not depend on PHP, all checks are done locally (no calls to the security.symfony.com API): $ symfony security:check TIP: If you are using Github, you can use the PHP Security Checker [Github Action] to automatically check for vulnerabilities when pushing code.
tag is a command line tool to manipulate tags on Mac OS X files (10.9 Mavericks and above), and to query for files with those tags. tag can use the file system's built-in metadata search functionality to rapidly find all files that have been tagged with a given set of tags.
A simple command-line arguments parsing library for Scala, written in spirit of Ruby's Trollop. Cross-built for Scala 2.10, 2.11, 2.12, 2.13 and support for Scala Native and Scala JS. Scallop supports:
Command line management for Google G Suite
Google Apps Manager or GAM is a free and open source command line tool for Google G Suite Administrators that allows them to manage many aspects of their Google Apps Account quickly and easily. With GAM you can create and manage users, groups and domains; manage email, security and calendar settings; manage admins and organizations and many more. To use GAM Google Apps Business, Education, Partner or Government Edition is required.
command line tool to manage email …
vmm is the easy to use and configurable command line tool for administrators and postmasters, to manage domains, alias-domains, accounts and relocated mail users. It allows the fast and easy management of mail servers. vmm is written in Python. It's designed for installations using Dovecot and Postfix with a PostgreSQL backend.
Create PDF from JPEG scans and photos
Cross-platform command-line tool for creation of PDF documents from scans/photos of pages in JPEG (.jpg) format and the lightest weight ANSI C library to put multiple JPEG files into one PDF file. You can add handwritten comments to PDF scans (over original images) with xournal: It supports graphics tablets and saves comments to PDFs as vector data.
Multi-connection command line tool to download Internet sites. Similar to wget and cURL, but it manages up to 50 parallel links. Main features are: recursive fetching, Metalink retrieving, segmented download and image filtering by width and height.
Gerber to PDF converter
Gerber2PDF is a command-line tool to convert Gerber files to PDF for proofing and hobbyist printing purposes. It converts multiple Gerber files at once, placing the resulting layers each on its own page within the PDF. Each layer has a PDF bookmark for easy reference. Layers can optionally be combined onto a single page and rendered with custom colors and transparency.
Xidel is a cli webpage scraping tool supporting XPath/XQuery 3 and CSS
Xidel is a command line tool to download web pages and extract data from them. This data can be extracted using XPath/XQuery 3.0 (with a compatibility modes for XPath 2.0 and XQuery 1.0), JSONiq, CSS 3 selectors, and custom, pattern-matching templates that are like an annotated version of the processed page. It can download files over HTTP/S connections, follow redirections, links, or extracted values, and also process local files. The extracted values can then be exported as plain text/XML/JSON, or assigned to variables to use in other extract expressions. It also provides an online CGI service for testing of XPath / XQuery 3.0 expression. (Xidel is a part of the VideLibri project, so its project page just redirects there )
Command line tool to convert BMP images to binary bitmaps and c header files with 8bit page layout instead of line layout (one byte is 8-bit vertical line). Can be used to present data for graphical LCD images in micro controller programming (eg AVR).
What's inside your mp3 files REALLY ?
mp3guessenc is based upon the original project by Naoki Shibata. This command line utility was born to detect the encoder used for a mpeg layer III file but now it can do more and scan any mpeg audio file (any layer) and print a LOT of useful information. Latest modifications include fixes, new features and code optimizations.
Portable command line utility for encoding and recording audio signals (chirps) to set the speed, incline, and resistance functions of iFit technology equipped exercise machines. Writes generated settings signals to music file format.
Bulk extractor for Ensoniq-formatted disk images
EnDiskEx is a command-line tool that bulk extracts instruments, sequences, songs, and banks from Ensoniq-formatted disk images (RAW, GKH, EDE, and EDA) for the EPS/ASR family of samplers. The extracted files are saved as EFE / SMF / TXT files. EnDiskEx is designed to extract Ensoniq banks for re-creation within a different DAW. It will track down the instrument and song files from bank references even if they were saved on another disk. There also exists a disk mapping feature to correct for any errors in this process caused by having relabeled disks, forgotten to label disks, etc. EnDiskEx has been tested and validated against a variety of RAW, GKH, EDE, and EDA images files the dev team has, including but not limited to, the ASR factory disks, the EPS 16+ factory disks, and the EPS (classic) factory disks.
A CLI audio cue file generator which uses the Discogs.com API
DCue is a command line tool for automatically generating audio cue sheets (.cue files) using the massive release database to find artist names, track titles, durations and other information via the Discogs API. DCue is equally compatible with Windows and Linux (and probably OS X -- though not officially supported). It has no external dependencies whatsoever. It makes use of some C++11 features where available.
Simplifies the use of the Filemaker Data Migration Tool
The Data Migration Tool Automator is tool for simplifying the use of the Filemaker Data Migration Tool (FDMT) . The FDMT is a command line tool published by Filemaker that facilitates the migration of data from an existing production database to a new clone version of the same database. For more information refer to: The problem with the FDMT is that it is a command line tool which requires long and complicated instructions to execute. It can take several attempts and a lot of time to get the exact instruction you need. The Filemaker Data Migration Tool Automator is a Filemaker database which makes it easy to create the command line syntax and calls the terminal scripts for the Filemaker Data Migration Tool. It simplifies the selection of the migration files, enter usernames and passwords and directs them to the FDMT.
For full, incremental, compressed and encrypted backups or archives
DAR is a command-line backup and archiving tool that uses selective compression (not compressing already compressed files), strong encryption, may split an archive in different files of given size and provides on-fly hashing, supports differential backup with or without binary delta, ftp and sftp protocols to remote cloud storage Archive internal's catalog, allows very quick restoration even a single file from a huge, eventually sliced, compressed, encrypted archive eventually located on a remote cloud storage, by only reading/fetching the necessary data to perform the operation. Dar saves *all* UNIX inode types, takes care of hard links, sparse files as well as Extended Attributes (MacOS X file forks, Linux ACL, SELinux tags, user attributes) and some Filesystem Specific Attributes (Linux ext2/3/4, Mac OS X HFS+) more details at:
Rainmaker is a command line pseudo random number generator designed to work on multiple platforms. Rainmaker can be used produce cryptographically strong non-blocking output in many formats (Base-16, Alphanumeric, Numeric , and Alpha only modes).
A minimalistic but complete standard Forth compiler in C
MinForth V3.4 is a classic Forth system with command-line interface. Development resource requirements are minimal. A source text editor and a C compiler are sufficient. By design no toolchain is required to adapt or rebuild MinForth. A complete rebuild takes only few seconds. Current sources are for Windows and Linux (32-bit or 64-bit). MinForth primitive definitions are written in mixed Forth and C language and are transpiled to pure C code. Main but not exclusive application for the transpiler is to build the MinForth V3.4 high-level Forth compiler. MinForth V3.4 is widely conformant to the Forth-2012 draft standard and passes the usual test suites. Feedback and bug reports are welcome per - Usenet forum forum/comp.lang.forth - email to
Small-K (Small Calculator) is a command line based mathematical expression evaluating engine in C. It supports symbolical extension in the forms of math functions with arbitrary number of arguments (e.g. f(1, 3)) and variables (e.g. PI).
DB Sanity performs checks on a database for verifying data consistency and correctness of aplication deployments. It is invoked by command line and creates an HTML report with aggregated diagnostic summaries and listings of faulty database entries.
Command-line tool for managing Amazon S3 and CloudFront services
Open-source tool to access Amazon S3 file storage. S3cmd is a free command-line tool and client for uploading, retrieving, and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage. Lots of features and options have been added to s3cmd since its very first release in 2008. Recently, more than 60 command-line options, including multipart uploads, encryption, incremental backup, s3 sync, ACL and Metadata management, S3 bucket size, bucket policies, and more, were counted.
The Nemesis Project is designed to be a command line based, portable human IP stack for UNIX-like and Windows systems. The suite is broken down by protocol, and should allow for useful scripting of injected packets from simple shell scripts.
TraceMAC is a command-line Layer 2 traceroute for Cisco switches
TraceMAC is a Windows/Linux command-line tool that allows you to trace a specific MAC address thru Cisco switches. It works by connecting to a switch using SSH, SNMP, Telnet, HTTP or HTTPS and do some "show commands" and later process the output, this will happen recursively until it finds the switch where that MAC address (PC/Printer/Etc) is directly connected. It works with Cisco switches only and you must have CDP enabled at least on trunks/links between switches! Tested with Cisco SW: 2960, 3560, 3750, 4948, 6509, Express 500. It uses Nbtscan.exe (NetBIOS) as a alternative method to discover the mac address of a host and now seems that it is considered a malware. Anyway it is just a simple network tool that can scan the network similar to NMAP or Angry IP Scanner, etc.
PacketFlow is a command line utility that processes an XML configuration to generate a set of firewall rules. It is intended to be installed and run directly on the firewall itself. PacketFlow was designed to deal with complex configurations.
A command-line windows application to manage wireless network connections, cards and profiles. Connect to WLANs, query for RSSI, stadistics... It can be used as an example of how to use Microsoft Native Wifi API dlls from any ANSI C compatible IDE
In the field of Command-line Tools learning from a live instructor-led and hand-on training courses would make a big difference as compared with watching a video learning materials. Participants must maintain focus and interact with the trainer for questions and concerns. In Qwikcourse, trainers and participants uses DaDesktop , a cloud desktop environment designed for instructors and students who wish to carry out interactive, hands-on training from distant physical locations.
For now, there are tremendous work opportunities for various IT fields. Most of the courses in Command-line Tools is a great source of IT learning with hands-on training and experience which could be a great contribution to your portfolio.
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