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• Dd (command)
  ; '''if'''=''file'' : Input File: Read from ''file'' instead from [[Redirection (Linux)|standard input]]. ; '''of'''=''file'' : Output File: Write to ''file'' instead to standard output. See also the keyword '''notrunc'''.
  10 KB (1,656 words) - 01:46, 7 May 2018
• Shred
  ...o hide its contents, and optionally delete it. It overwrites the specified FILE(s) repeatedly, in order to make it harder for even very expensive hardware * <tt>shred [OPTIONS] FILE [...]</tt>
  4 KB (623 words) - 02:39, 13 February 2007
• Tex2im
  The content of input file should be plain latex mathmode code. Alternatively, a string containing the ;<code>-o file</code> : specifies output filename, default is inputfile with new extension
  5 KB (868 words) - 07:48, 25 December 2008
• Awk/scripts
  ...<code>$1</code>, on the foo <code>foo1</code>, and the second field on the file <code>foo2</code>: *Append the output to the file <code>foo</code>:
  18 KB (2,772 words) - 22:57, 26 October 2021
• Glob()
  '''glob()''' is a Unix library function that expands file names using a pattern matching notation reminiscent of [[regular expression *[http://perldoc.perl.org/File/Glob.html Perl 'File::Glob' module]
  4 KB (646 words) - 01:43, 16 June 2012
• Linux HDD
  ...machine, you must add the appropriate line to your <code>/etc/fstab</code> file. Something ''like'' the following should work for most uses: Then mount it using the information in your <code>/etc/fstab</code> file:
  7 KB (1,275 words) - 03:45, 1 December 2015
• Pax
  ...''' - read and write file archives and copy directory hierarchies. A POSIX File System Archiver. It supports the two most common forms of standard Unix arc ...<code>a.pax</code> which are owned by root with group bin and preserve all file permissions:
  1 KB (251 words) - 04:20, 6 July 2012
• Update timezone files for earlier Daylight Savings Time
  ...load the [ftp://elsie.nci.nih.gov/pub/ patch from here]. You will need the file <code>tzdata2007c.tar.gz</code> (this may have changed since writing this). ...that tell us we have successfully updated our <code>/etc/localtime</code> file.
  5 KB (705 words) - 01:44, 14 May 2015
• Flash motherboard BIOS
  ...sure that you have support for the <code>vfat</code> and <code>loop</code> file systems in the kernel. Or you can have those features compiled as modules. Consult <code>/proc/fileystems</code> to see if you have the needed file systems supported. If you do, you should be able to "loop mount" the floppy
  3 KB (497 words) - 21:04, 11 March 2007
• Samba
  ...sername and password in a text file that anyone can read, you can create a file in, for an example, <code>/etc/samba/smbpasswd</code> with the following tw It is possible to set the mount uid, gid, and umasks for file/directory create/deletion/overwrite with the following set of options:
  5 KB (785 words) - 17:57, 8 May 2014
• PDB Validation Suite
  ''Note: The majority of this article was taken directly from the README file.'' For example, to create reports for a file in mmCIF format named <code>1xyz.cif</code> type:
  6 KB (895 words) - 02:37, 24 March 2007
• Iftab
  '''iftab''' - static information about the network interfaces. The file <code>/etc/iftab</code> contains descriptive information about the various ...s use <code>/etc/iftab</code>. For an example, openSUSE uses the following file.''
  6 KB (856 words) - 17:23, 3 January 2014
• Crontab
  ...eads a series of commands from [[standard input]] and collects them into a file also known as a "crontab" which is later read and whose instructions are ca export EDITOR=vi # to specify a editor to open crontab file.
  8 KB (1,304 words) - 08:49, 18 September 2021
• Binutils
  ...t code in various object file formats. The current versions use the Binary File Descriptor library (libbfd). They are typically used in conjunction with GN *<code>addr2line</code> &mdash; convert address to file and line
  2 KB (285 words) - 03:57, 1 April 2007
• Linux kernel
  * File management $ file /sbin/init
  6 KB (897 words) - 10:20, 17 November 2014
• RPM Package Manager
  NOTE: RPM file names normally have the following format: ...automatically compiled and installed, following instructions in the .spec file included in the SRPM.
  8 KB (1,064 words) - 22:36, 19 April 2023
• Recovery Is Possible
  ...leted files, by ignoring the filesystem and checking disk blocks for known file types
  3 KB (481 words) - 05:17, 2 April 2007
• Fstab
  ...how they are to be used or otherwise integrated into the overall system's file system. The following is an example of a fstab file on a Red Hat [[Linux]] system:
  6 KB (838 words) - 01:45, 3 April 2007
• Common Unix Printing System
  For example, a generic PPD file for all models of HP Color LaserJet contains: ...rators Manual, [http://www.cups.org/doc-1.1/sam.html#FILE_TYPING_FILTERING File Typing and Filtering]. (accessed 2007-01-09).</ref>
  6 KB (795 words) - 22:59, 23 January 2008
• List of GNU packages
  | [[File Transfer Protocol|ftp]], [[telnet]], [[rsh]], [[rlogin]], [[tftp]] | Archiver able to creates and handles file archives in various formats
  8 KB (1,101 words) - 05:31, 4 April 2007
• GRUB
  ...e>hd0,1</code> refers to hard drive 1 partition 2 where, for an example, a file system could be installed. You'll need to change those numbers if yours dif
  2 KB (303 words) - 23:30, 30 May 2012
• GNU General Public License
  to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least
  18 KB (2,945 words) - 22:54, 4 April 2007
• SoX
  ;<code>crossfade_cat.sh</code> : Crossfade two audio files into a single file. ;<code>fmsim</code> : Make an audio file sound like its playing over an FM radio
  4 KB (624 words) - 11:10, 28 October 2014
• GenBank
  ! colspan="7" bgcolor="#EFEFEF" | '''GenBank Flat File Release Statistics''' ...f name="gbrel">[ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt NCBI-GenBank Flat File - Distribution Release Notes] ('<code>gbrel.txt</code>').</ref>''<br/>
  9 KB (1,070 words) - 18:10, 1 April 2020
• A2ps
  ...enumerate if it is positive, e.g., `#10!f|$n|, |' lists only the ten first file names. If width is negative, then it does not enumerate the -width last obj file modification time in 24-hour format with seconds `hh:mm:ss'
  8 KB (1,389 words) - 23:23, 16 April 2007
• CDfs
  '''CDfs''' is a virtual Linux file system that provides access to individual data and audio tracks on compact *Red Book audio: Appears as a CDA file; reading from it will start the media player reading from the tracks. The C
  3 KB (492 words) - 02:50, 21 April 2007
• TLSMD
  ...[[Christoph Champ|Champ PC]], Merritt EA (2010). "[https://docs.google.com/file/d/0B7cFvC52gEb9MTRmNDQyNmYtZDVhNS00OTViLTkxZGItODk3ZmU2ZjdjYzM5/edit Valida *Modify <code>make.inc</code> file for your system. Below is an ''example'':
  15 KB (2,303 words) - 00:36, 13 July 2012
• Surface Racer
  ...s and void regions between surfaces from coordinate data supplied in a PDB file.
  3 KB (366 words) - 04:33, 9 April 2008
• List of EMBOSS programs
  ==Acd file utilities== ;acdtable : Creates an HTML table from an ACD file
  21 KB (2,762 words) - 01:04, 10 July 2012
• Pdbset (ccp4)
  ######################## Convert PDB file to mmCIF format
  2 KB (287 words) - 01:34, 9 July 2012
• List of ccp4 programs
  ==Coordinate file manipulations== ...bones2pdb.html bones2pdb] : Make a PDB pseudo-coordinate file from a bones file
  20 KB (3,274 words) - 01:27, 29 September 2007
• CCP4 (file format)
  ...:Category:ccp4|Collaborative Computational Project Number 4]] in 1979. The file format for electron density has become industry standard in [[:Category:Cry
  736 bytes (102 words) - 04:14, 25 April 2007
• PDB
  *[[wikipedia:Protein Data Bank (file format)]]
  6 KB (727 words) - 06:45, 25 April 2007
• Diffutils
  ...made independent changes to a common original; diff3 can produce a merged file that contains both persons' changes and warnings about conflicts.
  1 KB (218 words) - 17:47, 9 July 2012
• Gb2tab
  #REDIRECT [[Tab file format]]
  29 bytes (4 words) - 05:53, 4 May 2007
• List of SEALS programs
  ==simple fasta file manipulation== ;hotgi : hotlink gi numbers in any file
  10 KB (1,464 words) - 06:54, 4 May 2007
• Tar
  In computing, '''tar''' (derived from '''t'''ape '''ar'''chive) is both a file format (in the form of a type of archive bitstream) and the name of the pro % tar --index-file=foo.log -jcvf /dev/nst0 /data /home
  6 KB (968 words) - 05:29, 20 November 2013
• Gff2ps
  ...ion, but it also allows through a number of options and/or a configuration file, for a great degree of customization.<ref>Abril JF, Guigo R (2000). "gff2ps
  1 KB (175 words) - 00:58, 29 May 2007
• PNG
  ...ession. PNG was created to improve and replace the GIF format, as an image-file format not requiring a patent license. ...ed to indexed mode without changing the look of the image, while saving on file size. (See [[wikipedia:color depth]] for information on indexed mode and tr
  3 KB (443 words) - 03:33, 1 June 2007
• Littleutils
  ...e finder (repeats), image optimizers (opt-jpg opt-png opt-gif recomp-jpg), file rename tools (lowercase uppercase), archive recompressors (to-bzip to-7zip *<tt>lreplace</tt> &mdash; replace one string with another in a file.
  1 KB (149 words) - 01:42, 4 June 2007
• HOW file format
  The '''HOW file format''' (or just '''HOW file'''). A HOW file consists of entries containing one sequence each. Each entry has the follow
  5 KB (518 words) - 03:07, 24 June 2007
• Sequence logo
  ...codon/ Codon Usage Database] &mdash; data generated from NCBI-GenBank Flat File Release 156.0 [2006-10-15]; 32,775 organisms.
  3 KB (451 words) - 01:49, 4 August 2007
• GMOD
  ...DME-gff-files.html About GFF files] &mdash; shows how to convert different file formats.
  2 KB (312 words) - 08:41, 18 May 2008
• Column file format
  ...e is that many different kinds of information can be contained in the same file. Also converting this format into anything else should be simple. *[[Tab file format]]
  461 bytes (68 words) - 03:05, 24 June 2007
• Tab file format
  #REDIRECT [[TAB file format]]
  29 bytes (4 words) - 07:16, 29 June 2007
• Pic language
  ==Example PIC file== Create a file, <code>foo.pic</code>, with the following:
  2 KB (272 words) - 05:47, 3 July 2007
• Perl/Scripts
  ==Edit a file from the CLI using [[Perl]]== perl -p -i.bak -e 's|before|after|' filename # backup of original file 'filename.bak'
  14 KB (2,259 words) - 06:45, 24 September 2007
• Superpose
  ...ings in MMDB convention, and <code>[foo_out.pdb]</code> is optional output file. ....html NCONT]'' &mdash; analyses contacts between subsets of atoms in a PDB file.
  12 KB (1,750 words) - 20:02, 4 February 2009
• Gp
  ...s showing the gene map. If the -H option is specified, additionaly an IMAP file is created: this allowes the creation of clickable, graphical maps created ...d -35 and -10 boxes, as well in the +1 region of a given sequence (see the file "matryca" in the data/ directory, which is the same as the E. coli matrix p
  7 KB (1,108 words) - 02:04, 13 July 2012
• Subversion
  Most subcommands take file and/or directory arguments, recursing on the directories. If no arguments *Step 2: Set default permissions in the <code>.bashrc</code> file:
  3 KB (512 words) - 22:04, 22 August 2018
• Bash/scripts
  h # remove a trailing file name component, leaving only the head. t # remove all leading file name components, leaving the tail.
  5 KB (733 words) - 22:38, 21 September 2021
• Apache
  # Index file and Document Root (where the public files are located) # Custom log file locations
  3 KB (400 words) - 21:59, 17 May 2015
• Pfam
  ...a list of PDB identifiers, the header and the title records from that PDB file.
  15 KB (2,040 words) - 08:23, 8 September 2007
• BLAST
  ===Configuration file=== ...dalone BLAST to operate, you have will need to have a <code>.ncbirc</code> file that contains the following lines:
  15 KB (1,757 words) - 22:12, 9 July 2012
• Postfix
  The [http://www.postfix.org/postconf.5.html main.cf] file stores site specific Postfix configuration parameters while [http://www.pos ;<code>postcat</code>: show Postfix queue file contents
  2 KB (307 words) - 00:18, 3 October 2007
• Git
  ...<code>git log</code> for a specific function in a specific (e.g., Python) file: $ git log -L :<funcname>:<file>
  4 KB (633 words) - 00:38, 19 February 2021
• Python/NumPy
  *write a to specified file (fid), in either binary or ascii format depending on options *read array from specified file (binary or ascii)
  10 KB (1,665 words) - 23:53, 30 March 2017
• Ext3grep
  ...l/~carlo17/howto/undelete_ext3.html HOWTO recover deleted files on an ext3 file system]
  638 bytes (105 words) - 07:36, 9 May 2008
• Umask
  ...ntrols which of the file permissions will not be set for any newly created file. The user file-creation mask is set to mode. If mode begins with a digit, it is interprete
  2 KB (256 words) - 04:16, 14 April 2008
• Ack
  Search for PATTERN in each source file in the tree from cwd on down. If [FILES] is specified, then only those file ...be specified in ACK_OPTIONS environment variable or an <code>.ackrc</code> file. If you want no dependency on the environment, turn it off with --noenv.
  8 KB (1,112 words) - 00:03, 16 December 2012
• Potrace
  ..., or BMP format), and the default output is an encapsulated [[PostScript]] file (EPS). A typical use is to create EPS files from scanned data, such as comp
  1 KB (158 words) - 03:40, 16 July 2008
• Boxplot
  svg(file = "foo.svg", width = 2.5, height = 5, pointsize = 8)
  2 KB (229 words) - 21:39, 18 February 2009
• Python/tutorial
  bin() file() iter() property() tuple() ==File I/O==
  13 KB (1,871 words) - 18:37, 14 June 2012
• Awk/tips and tricks
  ...all the rows where the 5th column does not equal "<code>-1</code>" in the file <code>foo.txt</code>, cut out the resulting columns 1-5 among the resulting
  2 KB (288 words) - 17:25, 9 January 2010
• Rpmbuild
  *Make necessary changes to spec file, then execute: ==Example spec file==
  5 KB (859 words) - 21:46, 11 February 2010
• Xxd
  ...of decoding to standard output. Moreover, it can be used to perform binary file patching. *Print everything but the first three lines (hex 0x30 bytes) of file.
  4 KB (563 words) - 02:39, 31 May 2012
• Etckeeper
  ...ommit changes made to <code>/etc</code> during package upgrades. It tracks file metadata that revison control systems do not normally support, but that is
  2 KB (232 words) - 05:56, 8 July 2013
• BLAST+
  ;makeblastdb : Formats input FASTA file(s) into a BLAST database ;formatdb [1] : Convert FASTA formatted seqeucne file into BLAST database
  11 KB (1,473 words) - 00:05, 10 July 2012
• Exome Project
  *[http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Data File Formats FAQ]
  14 KB (1,969 words) - 21:46, 17 July 2012
• FASTQ format
  ...er''.<ref name="Cock et al 2009">Cock, ''et al.'' (2009). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ var A FASTQ file normally uses four lines per sequence. Line 1 begins with a '@' character a
  13 KB (1,841 words) - 01:53, 26 July 2012
• ELinks
  *Local file support *Mimetypes file support for mapping file extensions to content types [c]
  11 KB (1,694 words) - 20:05, 24 July 2012
• Socat
  ...NIX, IP4, IP6 - raw, UDP, TCP), an SSL socket, proxy CONNECT connection, a file descriptor (stdin etc.), the GNU line editor (readline), a program, or a co * file permissions;
  3 KB (439 words) - 05:15, 21 May 2014
• Checking for swappers on XenServer
  ...apdisk2 process that is responsible for identifying this <code>.vhd</code> file <code>`tap-ctl list`</code> will help you identify the <code>.vhd</code> file or the UUID of the VDI, which is responsible for the slice pushing heavy IO
  6 KB (868 words) - 04:49, 30 October 2013
• XenServer
  ;VHD : actual Virtual HDD file ends with this extension
  3 KB (441 words) - 23:12, 1 March 2015
• Rackspace API
  * Upload ("PUT") a file to a given container: $ CONTAINER=foo; curl -X PUT -T /path/to/your/local/file.txt -D - \
  38 KB (4,754 words) - 17:30, 19 September 2019
• Linux swap space
  ==Creating a swap file== *Create the file to be used for swap:
  3 KB (526 words) - 02:16, 14 January 2016
• Sar (sysstat)
  ...PU usage broken down by all cores for the 10day day of the month from sa10 file.
  6 KB (711 words) - 05:04, 28 July 2014
• Di (command)
  [file [...]] If file is specified, the usage information for the partition on which
  15 KB (2,072 words) - 19:07, 22 November 2013
• Xl (XenServer)
  ; <code>create</code> : Create a domain from config file <filename>
  6 KB (864 words) - 05:51, 25 December 2013
• Tcpdump
  * Capture the packets and write output to a binary file (useful for later analysis in, for example, [[wireshark]]): * Read the packets from a previously saved file (e.g., from the previous command):
  11 KB (1,707 words) - 16:48, 19 June 2015
• Cryptsetup
  *Create an encrypted file system on a given partition:
  1 KB (184 words) - 19:06, 5 May 2014
• Logical Volume Manager
  ...it persistent by adding the following line to your <code>/etc/fstab</code> file and test mount it (again):
  3 KB (413 words) - 18:52, 16 April 2015
• Netcat
  * Setting up a one-shot webserver on port 8080 to present the content of a file ..."HTTP/1.0 200 OK\r\nContent-Length: $(wc -c <some.file)\r\n\r\n"; cat some.file; } | nc -l 8080
  6 KB (1,051 words) - 00:04, 4 May 2014
• Selinux
  ...bleshoot: SELinux is preventing /usr/sbin/httpd from getattr access on the file /var/www/html/index.html. For complete SELinux messages. run sealert -l b31 ...bleshoot: SELinux is preventing /usr/sbin/httpd from getattr access on the file /var/www/html/index.html. For complete SELinux messages. run sealert -l b31
  2 KB (360 words) - 22:50, 8 September 2016
• Network Time Protocol
  ...r update the <code>restrict</code> line in your <code>/etc/ntp.conf</code> file:
  4 KB (668 words) - 21:38, 9 April 2018
• CentOS
  ...INPUT ...`</code>) or create/edit the <code>/etc/sysconfig/iptables</code> file to look something like the following (very basic with ports 22 and 80 open) If you are saving your rules in that <code>/etc/sysconfig/iptables</code> file, you will then need to run one of the following commands:
  6 KB (850 words) - 00:00, 27 August 2016
• Rkhunter
  * executables with anomalous file permissions;
  2 KB (298 words) - 21:38, 10 September 2021
• Xm (xen)
  ;<code>xm save</code> : Similar to suspend except with user definable state file ...in the config file. See <code>xmdomain.cfg</code> for full details of that file format, and possible options used in either the configfile or Name=Value co
  32 KB (5,154 words) - 10:30, 20 September 2014
• Sftp
  ...n of the [[SSH|Secure Shell protocol]] (SSH) version 2.0 to provide secure file transfer capability, but is also intended to be usable with other protocols ...Add the following to the bottom of your <code>/etc/ssh/sshd_config</code> file
  2 KB (415 words) - 11:40, 20 September 2014
• Linux log files
  :Alternative logs information from update-alternatives into this log file. :Access Log file &mdash; records incoming requests and all requests processed by Apache (e.g
  5 KB (718 words) - 00:58, 12 December 2018
• Ansible
  * Create your own custom Ansible configuration file: * Create your [http://docs.ansible.com/intro_inventory.html inventory file] and add it to your [[git]] repo (we will call our development group of hos
  12 KB (1,304 words) - 17:04, 10 April 2022
• Screen
  ...een settings according to our preferences using the <code>.screenrc</code> file. ...istophchamp/dnaomics/blob/master/admin/dotfiles/screenrc Example .screenrc file]
  5 KB (753 words) - 21:27, 3 August 2020
• Rackspace API/Cloud Networks
  ...new Cloud Network's configuration settings will be stored in the following file (it might not be "eth2" on your server):
  6 KB (784 words) - 17:29, 19 September 2019
• Pv
  <code>pv</code> will copy each supplied FILE in turn to standard output (- means standard input), or if no FILEs are spe * A simple example to watch how quickly a file is transferred using [[netcat|nc(1)]]:
  4 KB (537 words) - 22:16, 6 March 2015
• GNU parallel
  ...ring <code>bar</code>. The parallel command will work as expected unless a file name contains a newline. In order to avoid this limitation one may use: The above command uses the null character to delimit file names.
  3 KB (470 words) - 02:36, 20 March 2015
• MediaFire
  '''MediaFire''' is a file hosting, file synchronization, and cloud storage service.
  4 KB (409 words) - 22:09, 14 June 2015
• Strace
  ...ode>strace(1)</code> may reveal that the program is attempting to access a file which does not exist or cannot be read. open("/foo/bar", O_RDONLY) = -1 ENOENT (No such file or directory)
  6 KB (855 words) - 21:12, 18 February 2016
• Crudini
  * Create a test conf file:
  948 bytes (147 words) - 17:53, 27 October 2015
• PXE boot server
  * Make the <code>/etc/default/tftpd-hpa</code> file contain only the following lines: * Add the following line to the <code>/etc/inetd.conf</code> file:
  3 KB (495 words) - 22:24, 12 December 2015
• Sysctl
  ...a virtual file system, reading its contents, parsing them and closing the file. The sysctl system call does exist on Linux, but does not have a wrapping f ...sctl kernel parameter setting desired to the <code>/etc/sysctl.conf</code> file:
  3 KB (441 words) - 02:14, 14 January 2016

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