section 1 · User commands 💻

68502 pages · page 271 of 343

S (continued)

s6-mkfifo(1)create FIFOs, a.k.a. named pipes✨
s6-nice(1)execute into a program with an altered nice value✨
s6-nuke(1)send signals to every process it is allowed to send✨
s6-pause(1)block until killed✨
s6-printenv(1)print environment variables✨
s6-quote(1)quote a string and write it to stdout✨
s6-quote-filter(1)act as a filter, quoting lines read on stdin and writing the quoted lines to stdout✨
s6-rename(1)atomically rename a file✨
s6-rmrf(1)remove a file or directory tree entirely✨
s6-seq(1)print a sequence of numbers✨
s6-sleep(1)sleep for a given time, then optionally execute a program✨
s6-sort(1)sort input✨
s6-sync(1)flush all the dirty system buffers, and block until they're clean✨
s6-tai64ndiff(1)show time difference between two TAI64N-timestamped lines✨
s6-tail(1)print a file or its stdin after a certain number of bytes or lines✨
s6-touch(1)change the modification and access times of a file, creating it if it does not exist✨
s6-true(1)return 0✨
s6-uniquename(1)create a guaranteed unique file name and print it to stdout✨
s6-unquote(1)unquote a quoted string and write it to stdout✨
s6-unquote-filter(1)read quoted strings on stdin, unquote them and write the results to stdout✨
s6-update-symlinks(1)link the content of several similar directory trees under a single tree✨
s7(1)interpreter for the Seed7 programming language✨
s7c(1)compiler for the Seed7 programming language✨
s9(1)✨
s_client(13ssl)OpenSSL application commands✨
s_client(1ossl)OpenSSL application commands✨
s_client(1ssl)OpenSSL application commands✨
s_server(13ssl)OpenSSL application commands✨
s_server(1ossl)OpenSSL application commands✨
s_server(1ssl)OpenSSL application commands✨
s_time(13ssl)OpenSSL application commands✨
s_time(1ossl)OpenSSL application commands✨
s_time(1ssl)OpenSSL application commands✨
sa-awl(1)examine and manipulate SpamAssassin's auto-welcomelist db✨
sa-awl(1p)examine and manipulate SpamAssassin's auto-welcomelist db✨
sa-check_spamd(1)spamd monitoring script for use with Nagios, etc.✨
sa-check_spamd(1p)spamd monitoring script for use with Nagios, etc.✨
sa-compile(1)compile SpamAssassin ruleset into native code✨
sa-compile(1p)compile SpamAssassin ruleset into native code✨
sa-heatu(1)Spamasassin Heuristic Email Address Tracker Utility✨
sa-learn(1)train SpamAssassin's Bayesian classifier✨
sa-learn(1p)train SpamAssassin's Bayesian classifier✨
sa-update(1)automate SpamAssassin rule updates✨
sa-update(1p)automate SpamAssassin rule updates✨
sabcmd(1)a command line interface to Sablotron XSLT processor✨
sabnzbdplus(1)a web-based binary newsgrabber with nzb support.✨
sabredav(1)SabreDAV test server✨
sac2mseed(1)SAC to miniSEED converter✨
sacc(1)a terminal gopher client✨
sacct(1)displays accounting data for all jobs and job steps in the Slurm job accounting log or Slurm database✨
sacct-emulator(1)client programs to emulate the SLURM (Simple Linux Utility for Resource Management), an open-source cluster resource management and job scheduling.✨
sacctmgr(1)Used to view and modify Slurm account information.✨
sacctmgr-emulator(1)client programs to emulate the SLURM (Simple Linux Utility for Resource Management), an open-source cluster resource management and job scheduling.✨
sacd(1)Super Audio CD decoder✨
sachesi(1)Firmware Tools for BlackBerry OS 10✨
sact(1)show editing activity status of an SCCS file✨
sact(1p)print current SCCS file-editing activity (DEVELOPMENT)✨
sact(1posix)print current SCCS file-editing activity (DEVELOPMENT)✨
sada(1)slave authorization/deauthorization✨
sadf(1)Display data collected by sar in multiple formats.✨
sadt(1)simple DEP-8 test runner✨
safe-ldif(1)verify and dump an LDIF file for backup✨
safe-rm(1)wrapper around the rm command to prevent accidental deletions✨
safe-vdash(1)CLI tool to monitor nodes on the Safe Network✨
safecat(1)safely write data to a file✨
safecopy(1)rescue data from a source that causes IO errors✨
safeeyes(1)Safe Eyes✨
safekeep(1)Client/server backup script✨
saga_cmd(1)command-line interface to the System for Automated Geoscientific Analyses✨
saga_gui(1)graphical user interface to the System for Automated Geoscientific Analyses✨
sagcad(1)CAD/CAM of 2D program✨
sage(1)Open Source Mathematical Software✨
sage2psmcbor(1)Convert files in JSON Sage result format to files in a CBOR-derived format (psmCBOR)✨
sagoin(1)A command-line submission tool for the UMD CS Submit Server https://github.com/figsoda/sagoin✨
saidar(1)a curses-based tool for viewing system statistics✨
sailcut(1)a sail design and plotting package✨
saint-int-ctrl(1)support continuous measurements in SAINT✨
saint-reformat(1)imputs missing data and cleans up duplicate entries✨
saint-spc-ctrl(1)run SAINT with control data✨
saint-spc-noctrl(1)run SAINT scoring algorithm for protein-protein interaction data using label free quantitative proteomics data✨
saint-spc-noctrl-matrix(1)run SAINT for a (large-scale, matrix- formatted) dataset without control purification✨
sak(1)Slicing and dicing of FASTA/FASTQ files..✨
sakura(1)A simple but powerful libvte-based terminal emulator.✨
saldl(1)A lightweight well-featured CLI downloader optimized for speed and early preview.✨
salib(1)Sensitivity Analysis Library in Python. Contains Sobol, Morris, FAST, and other methods.✨
salliere(1)Duplicate Bridge Scorer✨
salloc(1)Obtain a Slurm job allocation (a set of nodes), execute a command, and then release the allocation when the command is finished.✨
salloc-emulator(1)client programs to emulate the SLURM (Simple Linux Utility for Resource Management), an open-source cluster resource management and job scheduling.✨
SalmID(1)rapid Kmer based Salmonella identifier from sequence data✨
salmon(1)highly-accurate, transcript-level quantification estimates from RNA-seq data✨
salmon-index(1)highly-accurate, transcript-level quantification estimates from RNA-seq data✨
salmon-quant(1)highly-accurate, transcript-level quantification estimates from RNA-seq data✨
salmon-swim(1)highly-accurate, transcript-level quantification estimates from RNA-seq data✨
salsa(1)tool to manipulate salsa projects, repositories and group members✨
salt(1)salt✨
salt-api(1)salt-api Command Start interfaces used to remotely connect to the salt master✨
salt-call(1)salt-call Documentation✨
salt-cloud(1)Salt Cloud Command Provision virtual machines in the cloud with Salt✨
salt-cp(1)salt-cp Documentation Copy a file or files to one or more minions✨
salt-key(1)salt-key Documentation✨
salt-lint(1)A command-line utility that checks for best practices in SaltStack.✨
salt-master(1)salt-master Documentation The Salt master daemon, used to control the Salt minions✨
salt-minion(1)salt-minion Documentation The Salt minion daemon, receives commands from a remote Salt master.✨
salt-pepper(1)Tool to access a salt-api instance✨
salt-proxy(1)salt-proxy Documentation✨
salt-run(1)salt-run Documentation Execute a Salt runner✨
salt-ssh(1)salt-ssh Documentation✨
salt-syndic(1)salt-syndic Documentation The Salt syndic daemon, a special minion that passes through commands from a higher master✨
salt-unity(1)salt-unity Command A unified invocation wrapper around other Salt CLI scripts.✨
sam(1)screen editor with structural regular expressions✨
sam(1plan9)screen editor with structural regular expressions✨
sam-stats(1)ea-utils: produce digested statistics✨
sam.save(1)screen editor with structural regular expressions✨
sam2bed(1)manual page for sam2bed 2.4.42+dfsg✨
sam2starch(1)manual page for sam2starch 2.4.42+dfsg✨
samba-log-parser(1)Samba (winbind) trace parser.✨
sambamba(1)toolkit for working with SAM/BAM files✨
sambamba-flagstat(1)getting flag statistics from BAM file✨
sambamba-index(1)tool for building standard index files for BAM data✨
sambamba-markdup(1)finding duplicate reads in BAM file✨
sambamba-merge(1)tool for merging several BAM files into one✨
sambamba-pileup(1)make a pileup✨
sambamba-slice(1)copying a slice of BAM file✨
sambamba-sort(1)tool for sorting BAM files✨
sambamba-view(1)tool for extracting information from SAM/BAM files✨
samblaster(1)post processing on an aligner (eg. bwa mem):✨
samclip(1)filter SAM file for soft and hard clipped alignments✨
samdump2(1)retrieves syskey and extract hashes from Windows 2k/NT/XP/Vista SAM.✨
sameboy-thumbnailer(1)create thumbnails from GameBoy ROMs✨
samefile(1)find identical files✨
samizdat-create-database(1)Samizdat database generation script✨
samizdat-import-feeds(1)update RSS feeds imported by hosted Samizdat sites✨
samizdat-role(1)Samizdat role management✨
samlsign(1)sign and verify XML documents✨
samp_hub(1)SAMP Hub Server✨
samplelibtransf(1)manual page for samplelibtransf libtransfer sample: Jul 14 2020 18:05:15✨
samplv1(1)an old-school polyphonic sampler synthesizer✨
samplv1_jack(1)an old-school polyphonic sampler synthesizer✨
samsung-mdc(1)Samsung Multiple Display Control Protocol✨
samterm(1)screen editor with structural regular expressions✨
samtools(1)Utilities for the Sequence Alignment/Map (SAM) format✨
samtools-addreplacerg(1)adds or replaces read group tags✨
samtools-ampliconclip(1)clip reads using a BED file✨
samtools-ampliconstats(1)produces statistics from amplicon sequencing alignment file✨
samtools-bedcov(1)reports coverage over regions in a supplied BED file✨
samtools-calmd(1)calculates MD and NM tags✨
samtools-cat(1)concatenate files together✨
samtools-checksum(1)produces checksums of SAM / BAM / CRAM content✨
samtools-collate(1)shuffles and groups reads together by their names✨
samtools-consensus(1)produces a consensus FASTA/FASTQ/PILEUP✨
samtools-coverage(1)produces a histogram or table of coverage per chromosome✨
samtools-cram-size(1)list a break down of data types in a CRAM file✨
samtools-depad(1)convert padded BAM to unpadded BAM✨
samtools-depth(1)computes the read depth at each position or region✨
samtools-dict(1)create a sequence dictionary file from a fasta file✨
samtools-faidx(1)indexes or queries regions from a fasta file✨
samtools-fasta(1)converts a SAM/BAM/CRAM file to FASTA or FASTQ✨
samtools-fastq(1)converts a SAM/BAM/CRAM file to FASTA or FASTQ✨
samtools-fixmate(1)fills in mate coordinates and insert size fields.✨
samtools-flags(1)convert between textual and numeric flag representation.✨
samtools-flagstat(1)counts the number of alignments for each FLAG type✨
samtools-fqidx(1)indexes or queries regions from a fastq file✨
samtools-head(1)view SAM/BAM/CRAM file headers✨
samtools-idxstats(1)reports alignment summary statistics✨
samtools-import(1)converts FASTQ files to unmapped SAM/BAM/CRAM✨
samtools-index(1)indexes SAM/BAM/CRAM files✨
samtools-markdup(1)mark duplicate alignments in a coordinate sorted file✨
samtools-merge(1)merges multiple sorted files into a single file✨
samtools-mpileup(1)produces "pileup" textual format from an alignment✨
samtools-phase(1)call and phase heterozygous SNPs✨
samtools-quickcheck(1)a rapid sanity check on input files✨
samtools-reference(1)extracts an embedded reference from a CRAM file✨
samtools-reheader(1)replaces the header in the input file✨
samtools-reset(1)removes the alignment information added by aligners and updates flags accordingly✨
samtools-rmdup(1)removes duplicate reads (obsolete)✨
samtools-samples(1)prints the samples from an alignment file✨
samtools-sort(1)sorts SAM/BAM/CRAM files✨
samtools-split(1)splits a file by read group.✨
samtools-stats(1)produces comprehensive statistics from alignment file✨
samtools-targetcut(1)cut fosmid regions (for fosmid pool only)✨
samtools-tview(1)display alignments in a curses-based interactive viewer.✨
samtools-view(1)views and converts SAM/BAM/CRAM files✨
samtools.pl(1)helper script for SAMtools✨
samu(1)ninja-compatible build tool✨
sancov-11(1)manual page for sancov 11✨
sancov-12(1)manual page for sancov 12✨
sancov-13(1)manual page for sancov 13✨
sancov-14(1)manual page for sancov 14✨
sancov-15(1)manual page for sancov 15✨
sancov-16(1)manual page for sancov 16✨
sancov-17(1)manual page for sancov 17✨
sancov-18(1)manual page for sancov 18✨
sancov-19(1)manual page for sancov 19✨
sancov-20(1)manual page for sancov 20✨
sancov-21(1)manual page for sancov 21✨
sancov-22(1)manual page for sancov 22✨
sand_align_kernel(1)align candidate sequences sequentially✨
sand_align_master(1)align candidate sequences in parallel✨
sand_compress_reads(1)compress sequence data✨
sand_filter_kernel(1)filter read sequences sequentially✨