Essential Skills for Bioinformatics: Unix/Linux PIPES a Simple Program with Grep and Pipes
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Name Synopsis Description
Perl version 5.10.0 documentation - vmsish NAME vmsish - Perl pragma to control VMS-specific language features SYNOPSIS use vmsish; use vmsish 'status';# or '$?' use vmsish 'exit'; use vmsish 'time'; use vmsish 'hushed'; no vmsish 'hushed'; vmsish::hushed($hush); use vmsish; no vmsish 'time'; DESCRIPTION If no import list is supplied, all possible VMS-specific features areassumed. Currently, there are four VMS-specific features available:'status' (a.k.a '$?'), 'exit', 'time' and 'hushed'. If you're not running VMS, this module does nothing. vmsish status This makes $? and system return the native VMS exit statusinstead of emulating the POSIX exit status. vmsish exit This makes exit 1 produce a successful exit (with status SS$_NORMAL),instead of emulating UNIX exit(), which considers exit 1 to indicatean error. As with the CRTL's exit() function, exit 0 is also mappedto an exit status of SS$_NORMAL, and any other argument to exit() isused directly as Perl's exit status. vmsish time This makes all times relative to the local time zone, instead of thedefault of Universal Time (a.k.a Greenwich Mean Time, or GMT). vmsish hushed This suppresses printing of VMS status messages to SYS$OUTPUT andSYS$ERROR if Perl terminates with an error status. and allowsprograms that are expecting "unix-style" Perl to avoid having to parseVMS error messages. It does not suppress any messages from Perlitself, just the messages generated by DCL after Perl exits. The DCLsymbol $STATUS will still have the termination status, but with ahigh-order bit set: EXAMPLE:$ perl -e"exit 44;" Non-hushed error exit%SYSTEM-F-ABORT, abort DCL message$ show sym $STATUS$STATUS == "%X0000002C" $ perl -e"use vmsish qw(hushed); exit 44;" Hushed error exit $ show sym $STATUS $STATUS == "%X1000002C" The 'hushed' flag has a global scope during compilation: the exit() ordie() commands that are compiled after 'vmsish hushed' will be hushedwhen they are executed. -
Package 'Slurmr'
Package ‘slurmR’ September 3, 2021 Title A Lightweight Wrapper for 'Slurm' Version 0.5-1 Description 'Slurm', Simple Linux Utility for Resource Management <https://slurm.schedmd.com/>, is a popular 'Linux' based software used to schedule jobs in 'HPC' (High Performance Computing) clusters. This R package provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to that found in the 'parallel' R package. The package also includes a method for creating socket cluster objects spanning multiple nodes that can be used with the 'parallel' package. Depends R (>= 3.3.0), parallel License MIT + file LICENSE BugReports https://github.com/USCbiostats/slurmR/issues URL https://github.com/USCbiostats/slurmR, https://slurm.schedmd.com/ Encoding UTF-8 RoxygenNote 7.1.1 Suggests knitr, rmarkdown, covr, tinytest Imports utils VignetteBuilder knitr Language en-US NeedsCompilation no Author George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>), Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), Michael Schubert [rev] (JOSS reviewer, <https://orcid.org/0000-0002-6862-5221>), Michel Lang [rev] (JOSS reviewer, <https://orcid.org/0000-0001-9754-0393>) Maintainer George Vega Yon <[email protected]> Repository CRAN Date/Publication 2021-09-03 04:20:02 UTC 1 2 expand_array_indexes R topics documented: expand_array_indexes . .2 JOB_STATE_CODES . .3 makeSlurmCluster . .4 new_rscript . .6 opts_slurmR . .7 parse_flags . .9 random_job_name . .9 read_sbatch . 10 slurmR . 11 slurmr_docker . 11 slurm_available . 12 Slurm_clean . 15 Slurm_collect . 16 Slurm_env . 17 Slurm_EvalQ . 18 slurm_job . 19 Slurm_log . 21 Slurm_Map . 22 snames . 25 sourceSlurm . 25 status . 28 the_plan . -
TEE Internal Core API Specification V1.1.2.50
GlobalPlatform Technology TEE Internal Core API Specification Version 1.1.2.50 (Target v1.2) Public Review June 2018 Document Reference: GPD_SPE_010 Copyright 2011-2018 GlobalPlatform, Inc. All Rights Reserved. Recipients of this document are invited to submit, with their comments, notification of any relevant patents or other intellectual property rights (collectively, “IPR”) of which they may be aware which might be necessarily infringed by the implementation of the specification or other work product set forth in this document, and to provide supporting documentation. The technology provided or described herein is subject to updates, revisions, and extensions by GlobalPlatform. This documentation is currently in draft form and is being reviewed and enhanced by the Committees and Working Groups of GlobalPlatform. Use of this information is governed by the GlobalPlatform license agreement and any use inconsistent with that agreement is strictly prohibited. TEE Internal Core API Specification – Public Review v1.1.2.50 (Target v1.2) THIS SPECIFICATION OR OTHER WORK PRODUCT IS BEING OFFERED WITHOUT ANY WARRANTY WHATSOEVER, AND IN PARTICULAR, ANY WARRANTY OF NON-INFRINGEMENT IS EXPRESSLY DISCLAIMED. ANY IMPLEMENTATION OF THIS SPECIFICATION OR OTHER WORK PRODUCT SHALL BE MADE ENTIRELY AT THE IMPLEMENTER’S OWN RISK, AND NEITHER THE COMPANY, NOR ANY OF ITS MEMBERS OR SUBMITTERS, SHALL HAVE ANY LIABILITY WHATSOEVER TO ANY IMPLEMENTER OR THIRD PARTY FOR ANY DAMAGES OF ANY NATURE WHATSOEVER DIRECTLY OR INDIRECTLY ARISING FROM THE IMPLEMENTATION OF THIS SPECIFICATION OR OTHER WORK PRODUCT. Copyright 2011-2018 GlobalPlatform, Inc. All Rights Reserved. The technology provided or described herein is subject to updates, revisions, and extensions by GlobalPlatform. -
Powerview Command Reference
PowerView Command Reference TRACE32 Online Help TRACE32 Directory TRACE32 Index TRACE32 Documents ...................................................................................................................... PowerView User Interface ............................................................................................................ PowerView Command Reference .............................................................................................1 History ...................................................................................................................................... 12 ABORT ...................................................................................................................................... 13 ABORT Abort driver program 13 AREA ........................................................................................................................................ 14 AREA Message windows 14 AREA.CLEAR Clear area 15 AREA.CLOSE Close output file 15 AREA.Create Create or modify message area 16 AREA.Delete Delete message area 17 AREA.List Display a detailed list off all message areas 18 AREA.OPEN Open output file 20 AREA.PIPE Redirect area to stdout 21 AREA.RESet Reset areas 21 AREA.SAVE Save AREA window contents to file 21 AREA.Select Select area 22 AREA.STDERR Redirect area to stderr 23 AREA.STDOUT Redirect area to stdout 23 AREA.view Display message area in AREA window 24 AutoSTOre .............................................................................................................................. -
Xshell 6 User Guide Secure Terminal Emualtor
Xshell 6 User Guide Secure Terminal Emualtor NetSarang Computer, Inc. Copyright © 2018 NetSarang Computer, Inc. All rights reserved. Xshell Manual This software and various documents have been produced by NetSarang Computer, Inc. and are protected by the Copyright Act. Consent from the copyright holder must be obtained when duplicating, distributing or citing all or part of this software and related data. This software and manual are subject to change without prior notice for product functions improvement. Xlpd and Xftp are trademarks of NetSarang Computer, Inc. Xmanager and Xshell are registered trademarks of NetSarang Computer, Inc. Microsoft Windows is a registered trademark of Microsoft. UNIX is a registered trademark of AT&T Bell Laboratories. SSH is a registered trademark of SSH Communications Security. Secure Shell is a trademark of SSH Communications Security. This software includes software products developed through the OpenSSL Project and used in OpenSSL Toolkit. NetSarang Computer, Inc. 4701 Patrick Henry Dr. BLDG 22 Suite 137 Santa Clara, CA 95054 http://www.netsarang.com/ Contents About Xshell ............................................................................................................................................... 1 Key Functions ........................................................................................................... 1 Minimum System Requirements .................................................................................. 3 Install and Uninstall .................................................................................................. -
UNIX X Command Tips and Tricks David B
SESUG Paper 122-2019 UNIX X Command Tips and Tricks David B. Horvath, MS, CCP ABSTRACT SAS® provides the ability to execute operating system level commands from within your SAS code – generically known as the “X Command”. This session explores the various commands, the advantages and disadvantages of each, and their alternatives. The focus is on UNIX/Linux but much of the same applies to Windows as well. Under SAS EG, any issued commands execute on the SAS engine, not necessarily on the PC. X %sysexec Call system Systask command Filename pipe &SYSRC Waitfor Alternatives will also be addressed – how to handle when NOXCMD is the default for your installation, saving results, and error checking. INTRODUCTION In this paper I will be covering some of the basics of the functionality within SAS that allows you to execute operating system commands from within your program. There are multiple ways you can do so – external to data steps, within data steps, and within macros. All of these, along with error checking, will be covered. RELEVANT OPTIONS Execution of any of the SAS System command execution commands depends on one option's setting: XCMD Enables the X command in SAS. Which can only be set at startup: options xcmd; ____ 30 WARNING 30-12: SAS option XCMD is valid only at startup of the SAS System. The SAS option is ignored. Unfortunately, ff NOXCMD is set at startup time, you're out of luck. Sorry! You might want to have a conversation with your system administrators to determine why and if you can get it changed. -
Lab Work 06. Linux Shell. Files Globbing & Streams Redirection
LAB WORK 06. LINUX SHELL. FILES GLOBBING & STREAMS REDIRECTION. 1. PURPOSE OF WORK • Learn to use shell file globbing (wildcard); • Learn basic concepts about standard UNIX/Linux streams redirections; • Acquire skills of working with filter-programs. • Get experience in creating composite commands that have a different functional purpose than the original commands. 2. TASKS FOR WORK NOTE. Start Your UbuntuMini Virtual Machine on your VirtualBox. You need only Linux Terminal to complete the lab tasks. Before completing the tasks, make a Snapshot of your Virtual Linux. If there are problems, you can easily go back to working condition! 2.0. Create new User account for this Lab Work. • Login as student account (user with sudo permissions). • Create new user account, example stud. Use adduser command. (NOTE. You can use the command “userdel –rf stud” to delete stud account from your Linux.) $ sudo adduser stud • Logout from student account (logout) and login as stud. 2.1. Shell File Globbing Study. 2.2. File Globbing Practice. (Fill in a Table 1 and Table 2) 2.3. Command I/O Redirection Study. 2.4. Redirection Practice. (Fill in a Table 3 and Table 4) © Yuriy Shamshin, 2021 1/20 3. REPORT Make a report about this work and send it to the teacher’s email (use a docx Report Blank). REPORT FOR LAB WORK 06: LINUX SHELL. FILES GLOBBING & STREAMS REDIRECTION Student Name Surname Student ID (nV) Date 3.1. Insert Completing Table 1. File globbing understanding. 3.2. Insert Completing Table 2. File globbing creation. 3.3. Insert Completing Table 3. Command I/O redirection understanding. -
HP Openvms Utility Routines Manual
HP OpenVMS Utility Routines Manual Order Number: BA554-90019 June 2010 This manual describes the OpenVMS utility routines, a set of routines that provide a programming interface to various OpenVMS utilities. Revision/Update Information: This manual supersedes the HP OpenVMS Utility Routines Manual, OpenVMS Alpha Version 8.3. Software Version: OpenVMS Version 8.4 for Integrity servers OpenVMS Alpha Version 8.4 Hewlett-Packard Company Palo Alto, California © Copyright 2010 Hewlett-Packard Development Company, L.P. Confidential computer software. Valid license from HP required for possession, use or copying. Consistent with FAR 12.211 and 12.212, Commercial Computer Software, Computer Software Documentation, and Technical Data for Commercial Items are licensed to the U.S. Government under vendor’s standard commercial license. The information contained herein is subject to change without notice. The only warranties for HP products and services are set forth in the express warranty statements accompanying such products and services. Nothing herein should be construed as constituting an additional warranty. HP shall not be liable for technical or editorial errors or omissions contained herein. Intel and Itanium are trademarks or registered trademarks of Intel Corporation or its subsidiaries in the United States and other countries. ZK4493 The HP OpenVMS documentation set is available on CD. This document was prepared using DECdocument, Version 3.3-1B. Contents Preface ............................................................ xvii 1 Introduction to Utility Routines 2 Access Control List (ACL) Editor Routine 2.1 Introduction to the ACL Editor Routine ........................... ACL–1 2.2 Using the ACL Editor Routine: An Example ....................... ACL–1 2.3 ACL Editor Routine . ........................................ ACL–2 ACLEDIT$EDIT ........................................... -
CS2043 - Unix Tools & Scripting Cornell University, Spring 20141
CS2043 - Unix Tools & Scripting Cornell University, Spring 20141 Instructor: Bruno Abrahao January 31, 2014 1 Slides evolved from previous versions by Hussam Abu-Libdeh and David Slater Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Vim: Tip of the day! Line numbers Displays line number in Vim: :set nu Hides line number in Vim: :set nonu Goes to line number: :line number Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Counting wc How many lines of code are in my new awesome program? How many words are in this document? Good for bragging rights Word, Character, Line, and Byte count with wc wc -l : count the number of lines wc -w : count the number of words wc -m : count the number of characters wc -c : count the number of bytes Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Sorting sort Sorts the lines of a text file alphabetically. sort -ru file sorts the file in reverse order and deletes duplicate lines. sort -n -k 2 -t : file sorts the file numerically by using the second column, separated by a colon Example Consider a file (numbers.txt) with the numbers 1, 5, 8, 11, 62 each on a separate line, then: $ sort numbers.txt $ sort numbers.txt -n 1 1 11 5 5 8 62 11 8 62 Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting uniq uniq uniq file - Discards all but one of successive identical lines uniq -c file - Prints the number of successive identical lines next to each line Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Character manipulation! The Translate Command tr [options] <char_list1> [char_list2] Translate or delete characters char lists are strings of characters By default, searches for characters in char list1 and replaces them with the ones that occupy the same position in char list2 Example: tr 'AEIOU' 'aeiou' - changes all capital vowels to lower case vowels Instructor: Bruno Abrahao CS2043 - Unix Tools & Scripting Pipes and redirection tr only receives input from standard input (stdin) i.e. -
Lecture 4: September 13 4.1 Process State
CMPSCI 377 Operating Systems Fall 2012 Lecture 4: September 13 Lecturer: Prashant Shenoy TA: Sean Barker & Demetre Lavigne 4.1 Process State 4.1.1 Process A process is a dynamic instance of a computer program that is being sequentially executed by a computer system that has the ability to run several computer programs concurrently. A computer program itself is just a passive collection of instructions, while a process is the actual execution of those instructions. Several processes may be associated with the same program; for example, opening up several windows of the same program typically means more than one process is being executed. The state of a process consists of - code for the running program (text segment), its static data, its heap and the heap pointer (HP) where dynamic data is kept, program counter (PC), stack and the stack pointer (SP), value of CPU registers, set of OS resources in use (list of open files etc.), and the current process execution state (new, ready, running etc.). Some state may be stored in registers, such as the program counter. 4.1.2 Process Execution States Processes go through various process states which determine how the process is handled by the operating system kernel. The specific implementations of these states vary in different operating systems, and the names of these states are not standardised, but the general high-level functionality is the same. When a process is first started/created, it is in new state. It needs to wait for the process scheduler (of the operating system) to set its status to "new" and load it into main memory from secondary storage device (such as a hard disk or a CD-ROM). -
Lock-Free Programming
Lock-Free Programming Geoff Langdale L31_Lockfree 1 Desynchronization ● This is an interesting topic ● This will (may?) become even more relevant with near ubiquitous multi-processing ● Still: please don’t rewrite any Project 3s! L31_Lockfree 2 Synchronization ● We received notification via the web form that one group has passed the P3/P4 test suite. Congratulations! ● We will be releasing a version of the fork-wait bomb which doesn't make as many assumptions about task id's. – Please look for it today and let us know right away if it causes any trouble for you. ● Personal and group disk quotas have been grown in order to reduce the number of people running out over the weekend – if you try hard enough you'll still be able to do it. L31_Lockfree 3 Outline ● Problems with locking ● Definition of Lock-free programming ● Examples of Lock-free programming ● Linux OS uses of Lock-free data structures ● Miscellanea (higher-level constructs, ‘wait-freedom’) ● Conclusion L31_Lockfree 4 Problems with Locking ● This list is more or less contentious, not equally relevant to all locking situations: – Deadlock – Priority Inversion – Convoying – “Async-signal-safety” – Kill-tolerant availability – Pre-emption tolerance – Overall performance L31_Lockfree 5 Problems with Locking 2 ● Deadlock – Processes that cannot proceed because they are waiting for resources that are held by processes that are waiting for… ● Priority inversion – Low-priority processes hold a lock required by a higher- priority process – Priority inheritance a possible solution L31_Lockfree -
Waste Transfer Stations: a Manual for Decision-Making Acknowledgments
Waste Transfer Stations: A Manual for Decision-Making Acknowledgments he Office of Solid Waste (OSW) would like to acknowledge and thank the members of the Solid Waste Association of North America Focus Group and the National Environmental Justice Advisory Council Waste Transfer Station Working Group for reviewing and providing comments on this draft document. We would also like to thank Keith Gordon of Weaver Boos & Gordon, Inc., for providing a technical Treview and donating several of the photographs included in this document. Acknowledgements i Contents Acknowledgments. i Introduction . 1 What Are Waste Transfer Stations?. 1 Why Are Waste Transfer Stations Needed?. 2 Why Use Waste Transfer Stations? . 3 Is a Transfer Station Right for Your Community? . 4 Planning and Siting a Transfer Station. 7 Types of Waste Accepted . 7 Unacceptable Wastes . 7 Public Versus Commercial Use . 8 Determining Transfer Station Size and Capacity . 8 Number and Sizing of Transfer Stations . 10 Future Expansion . 11 Site Selection . 11 Environmental Justice Considerations . 11 The Siting Process and Public Involvement . 11 Siting Criteria. 14 Exclusionary Siting Criteria . 14 Technical Siting Criteria. 15 Developing Community-Specific Criteria . 17 Applying the Committee’s Criteria . 18 Host Community Agreements. 18 Transfer Station Design and Operation . 21 Transfer Station Design . 21 How Will the Transfer Station Be Used? . 21 Site Design Plan . 21 Main Transfer Area Design. 22 Types of Vehicles That Use a Transfer Station . 23 Transfer Technology . 25 Transfer Station Operations. 27 Operations and Maintenance Plans. 27 Facility Operating Hours . 32 Interacting With the Public . 33 Waste Screening . 33 Emergency Situations . 34 Recordkeeping. 35 Environmental Issues.