bwa – Burrows-Wheeler Alignment Tool Synopsisbwa index ref.fa bwa mem ref.fa reads.fq > aln-se.sam bwa mem ref.fa read1.fq read2.fq > aln-pe.sam bwa aln ref.fa short_read.fq > aln_sa.sai bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam bwa bwasw ref.fa long_read.fq > aln.sam DescriptionBWA is a software package for…
BusyBox – The Swiss Army Knife of Embedded Linux Syntax busybox <applet> [arguments…] # or <applet> [arguments…] # if symlinkedDescriptionBusyBox combines tiny versions of many common UNIX utilities into a single small executable. It provides minimalist replacements for most of the utilities you usually find in GNU coreutils, util-linux, etc. The utilities in BusyBox generally…
busctl – Introspect the bus Synopsis busctl [OPTIONS…] [COMMAND] [NAME…]Descriptionbusctl may be used to introspect and monitor the D-Bus bus. CommandsThe following commands are understood: list Show all peers on the bus, by their service names. By default, shows both unique and well-known names, but this may be changed with the –unique and –acquired switches….
burst – explode digests into messages Synopsis burst [+folder] [msgs] [-inplace | -noinplace] [-mime | -nomime] [-automime] [-quiet | -noquiet] [-verbose | -noverbose] [-version] [-help]DescriptionBurst considers the specified messages in the named folder to be Internet digests, and explodes them in that folder. If -inplace is given, each digest is replaced by the “table of…
bzip2, bunzip2 – a block-sorting file compressor, v1.0.8 bzcat – decompresses files to stdout bzip2recover – recovers data from damaged bzip2 files Synopsisbzip2 [ -cdfkqstvzVL123456789 ] [ filenames … ] bzip2 [ -h|–help ] bunzip2 [ -fkvsVL ] [ filenames … ] bunzip2 [ -h|–help ] bzcat [ -s ] [ filenames … ] bzcat…
bundledoc – bundle all the files needed by a LaTeX document Synopsisbundledoc [–version] [–help] [—[no]verbose] [–texfile=file.tex] [–directory=directory] [—[no]localonly] [–exclude=string] [–include=filespec] [–manifest=file] [—listdeps=[yes|no|only|rel]…] [—[no]keepdirs] [–config=file.cfg] file.dep Descriptionbundledoc is a post-processor for the snapshot package that bundles together all the classes, packages, and files needed to build a given LaTeX document. It reads the .dep file that…
bundle – Ruby Dependency Management Synopsisbundle COMMAND [–no-color] [–verbose] [ARGS] DescriptionBundler manages an application’s dependencies through its entire life across many machines systematically and repeatably. See the bundler website https://bundler.io for information on getting started, and Gemfile(5) for more information on the Gemfile format. Options–no-color Print all output without color –retry, -r Specify the number…
bundle-viz – Generates a visual dependency graph for your Gemfile Synopsisbundle viz [–file=FILE] [–format=FORMAT] [–requirements] [–version] [–without=GROUP GROUP] Descriptionviz generates a PNG file of the current Gemfile(5) as a dependency graph. viz requires the ruby-graphviz gem (and its dependencies). The associated gems must also be installed via bundle install(1) bundle-install.1.html. Options–file, -f The name to…
bundle-update – Update your gems to the latest available versions Synopsisbundle update *gems [–all] [–group=NAME] [–source=NAME] [–local] [–ruby] [–bundler[=VERSION]] [–full-index] [–jobs=JOBS] [–quiet] [–patch|–minor|–major] [–redownload] [–strict] [–conservative] DescriptionUpdate the gems specified (all gems, if –all flag is used), ignoring the previously installed gems specified in the Gemfile.lock. In general, you should use bundle install(1) bundle-install.1.html to…
bundle-show – Shows all the gems in your bundle, or the path to a gem Synopsisbundle show [GEM] [–paths] DescriptionWithout the [GEM] option, show will print a list of the names and versions of all gems that are required by your [Gemfile(5)][Gemfile(5)], sorted by name. Calling show with [GEM] will list the exact location of…
bundle-remove – Removes gems from the Gemfile Synopsisbundle remove [GEM [GEM …]] [–install] DescriptionRemoves the given gems from the Gemfile while ensuring that the resulting Gemfile is still valid. If a gem cannot be removed, a warning is printed. If a gem is already absent from the Gemfile, and error is raised. Options–install Runs bundle…
bundle-pristine – Restores installed gems to their pristine condition Synopsisbundle pristine Descriptionpristine restores the installed gems in the bundle to their pristine condition using the local gem cache from RubyGems. For git gems, a forced checkout will be performed. For further explanation, bundle pristine ignores unpacked files on disk. In other words, this command utilizes…
bundle-platform – Displays platform compatibility information Synopsisbundle platform [–ruby] Descriptionplatform will display information from your Gemfile, Gemfile.lock, and Ruby VM about your platform. For instance, using this Gemfile(5): source "https://rubygems.org" ruby "1.9.3" gem "rack" If you run bundle platform on Ruby 1.9.3, it will display the following output: Your platform is: x86_64-linux Your app has…
bundle-package – Package your needed .gem files into your application Synopsisbundle package DescriptionCopy all of the .gem files needed to run the application into the vendor/cache directory. In the future, when running [bundle install(1)][bundle-install], use the gems in the cache in preference to the ones on rubygems.org. Git And Path GemsSince Bundler 1.2, the bundle…
bundle-outdated – List installed gems with newer versions available Synopsisbundle outdated [GEM] [–local] [–pre] [–source] [–strict] [–parseable | –porcelain] [–group=GROUP] [–groups] [–update-strict] [–patch|–minor|–major] [–filter-major] [–filter-minor] [–filter-patch] [–only-explicit] DescriptionOutdated lists the names and versions of gems that have a newer version available in the given source. Calling outdated with [GEM [GEM]] will only check for newer…
bundle-open – Opens the source directory for a gem in your bundle Synopsisbundle open [GEM] DescriptionOpens the source directory of the provided GEM in your editor. For this to work the EDITOR or BUNDLER_EDITOR environment variable has to be set. Example: bundle open ‘rack’ Will open the source directory for the ‘rack’ gem in your…
bundle-lock – Creates / Updates a lockfile without installing Synopsisbundle lock [–update] [–local] [–print] [–lockfile=PATH] [–full-index] [–add-platform] [–remove-platform] [–patch] [–minor] [–major] [–strict] [–conservative] DescriptionLock the gems specified in Gemfile. Options–update=<*gems> Ignores the existing lockfile. Resolve then updates lockfile. Taking a list of gems or updating all gems if no list is given. –local Do not…
bundle-list – List all the gems in the bundle Synopsisbundle list [–name-only] [–paths] [–without-group=GROUP] [–only-group=GROUP] DescriptionPrints a list of all the gems in the bundle including their version. Example: bundle list –name-only bundle list –paths bundle list –without-group test bundle list –only-group dev bundle list –only-group dev –paths Options–name-only Print only the name of each…
bundle-install – Install the dependencies specified in your Gemfile Synopsisbundle install [–binstubs[=DIRECTORY]] [–clean] [–deployment] [–frozen] [–full-index] [–gemfile=GEMFILE] [–jobs=NUMBER] [–local] [–no-cache] [–no-prune] [–path PATH] [–quiet] [–redownload] [–retry=NUMBER] [–shebang] [–standalone[=GROUP[ GROUP…]]] [–system] [–trust-policy=POLICY] [–with=GROUP[ GROUP…]] [–without=GROUP[ GROUP…]] DescriptionInstall the gems specified in your Gemfile(5). If this is the first time you run bundle install (and a Gemfile.lock…
bundle-inject – Add named gem(s) with version requirements to Gemfile Synopsisbundle inject [GEM] [VERSION] DescriptionAdds the named gem(s) with their version requirements to the resolved [Gemfile(5)][Gemfile(5)]. This command will add the gem to both your [Gemfile(5)][Gemfile(5)] and Gemfile.lock if it isn’t listed yet. Example: bundle install bundle inject ‘rack’ ‘> 0’ This will inject the…