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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26395?offset=30</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11735/search-shell-command-history</guid>
	<pubDate>Thu, 12 Jun 2014 17:43:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11735/search-shell-command-history</link>
	<title><![CDATA[Search Shell Command History]]></title>
	<description><![CDATA[<p>We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it? <br /><br />Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.</p><p><br /><strong>Shell history search command</strong><br /><br />Type history at a shell prompt:<br />$ history</p><p>It will display the list of all used commandline history with an serial number.<br /><br />To search particular command, enter:<br />$ history | grep command-name<br />$ history | egrep -i 'scp|ssh|ftp'<br />Emacs Line-Edit Mode Command History Searching<br /><br />To get previous command containing string, hit [CTRL]+[r] followed by search string:<br /><br />(reverse-i-search): <br /><br />To get previous command, hit [CTRL]+[p]. You can also use up arrow key.<br /><br />CTRL-p<br /><br />To get next command, hit [CTRL]+[n]. You can also use down arrow key.<br /><br />CTRL-n<br /><br /></p><p><strong>fc command</strong></p><p>Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.</p><p>For example list last 10 command, enter:<br />$ fc -l 10<br />To list commands 130 through 150, enter:<br />$ fc -l 130 150<br />To list all commands since the last command beginning with ssh, enter:<br />$ fc -l ssh<br />You can edit commands 1 through 5 using vi text editor, enter:<br />$ fc -e vi 1 5</p><p><strong>Delete command history</strong><br /><br />The -c option causes the history list to be cleared by deleting all of the entries:<br />$ history -c</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/35525/linux-commands-cheat-sheet-for-bioinformatics-and-computational-biology-professionals</guid>
	<pubDate>Mon, 05 Feb 2018 18:50:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/35525/linux-commands-cheat-sheet-for-bioinformatics-and-computational-biology-professionals</link>
	<title><![CDATA[Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals]]></title>
	<description><![CDATA[<p><span>The purpose of this cheat sheet is to introduce biologist and bioinformatician to the frequently used tools for NGS analysis as well as giving experience in writing one-liners.</span></p><ul>
<li><span></span><span><strong>File System</strong></span><span><strong><br /> </strong></span><span>ls</span><span>&nbsp;&mdash; list items in current directory</span><span><br /> </span><span>ls -l</span><span>&nbsp;&mdash; list items in current directory and show in long format to see perimissions, size, and modification date</span><span><br /> </span><span>ls -a</span><span>&nbsp;&mdash; list all items in current directory, including hidden files</span><span><br /> </span><span>ls -F</span><span>&nbsp;&mdash; list all items in current directory and show directories with a slash and executables with a star</span><span><br /> </span><span>ls dir</span><span>&nbsp;&mdash; list all items in directory dir</span><span><br /> </span><span>cd dir</span><span>&nbsp;&mdash; change directory to dir</span><span><br /> </span><span>cd ..</span><span>&nbsp;&mdash; go up one directory</span><span><br /> </span><span>cd /</span><span>&nbsp;&mdash; go to the root directory</span><span><br /> </span><span>cd ~</span><span>&nbsp;&mdash; go to to your home directory</span><span><br /> </span><span>cd -</span><span>&nbsp;&mdash; go to the last directory you were just in</span><span><br /> </span><span>pwd</span><span>&nbsp;&mdash; show present working directory</span><span><br /> </span><span>mkdir dir</span><span>&nbsp;&mdash; make directory dir</span><span><br /> </span><span>rm file</span><span>&nbsp;&mdash; remove file</span><span><br /> </span><span>rm -r dir</span><span>&nbsp;&mdash; remove directory dir recursively</span><span><br /> </span><span>cp file1 file2</span><span>&nbsp;&mdash; copy file1 to file2</span><span><br /> </span><span>cp -r dir1 dir2</span><span>&nbsp;&mdash; copy directory dir1 to dir2 recursively</span><span><br /> </span><span>mv file1 file2</span><span>&nbsp;&mdash; move (rename) file1 to file2</span><span><br /> </span><span>ln -s file link</span><span>&nbsp;&mdash; create symbolic link to file</span><span><br /> </span><span>touch file</span><span>&nbsp;&mdash; create or update file</span><span><br /> </span><span>cat file</span><span>&nbsp;&mdash; output the contents of file</span><span><br /> </span><span>less file</span><span>&nbsp;&mdash; view file with page navigation</span><span><br /> </span><span>head file</span><span>&nbsp;&mdash; output the first 10 lines of file</span><span><br /> </span><span>tail file</span><span>&nbsp;&mdash; output the last 10 lines of file</span><span><br /> </span><span>tail -f file</span><span>&nbsp;&mdash; output the contents of file as it grows, starting with the last 10 lines</span><span><br /> </span><span>vim file</span><span>&nbsp;&mdash; edit file</span><span><br /> </span><span>alias name 'command'</span><span>&nbsp;&mdash; create an alias for a command</span><span><br /> </span></li>
<li><span></span><span><strong>System</strong></span><span><strong><br /> </strong></span><span>shutdown</span><span>&nbsp;&mdash; shut down machine</span><span><br /> </span><span>reboot</span><span>&nbsp;&mdash; restart machine</span><span><br /> </span><span>date</span><span>&nbsp;&mdash; show the current date and time</span><span><br /> </span><span>whoami</span><span>&nbsp;&mdash; who you are logged in as</span><span><br /> </span><span>finger user</span><span>&nbsp;&mdash; display information about user</span><span><br /> </span><span>man command</span><span>&nbsp;&mdash; show the manual for command</span><span><br /> </span><span>df</span><span>&nbsp;&mdash; show disk usage</span><span><br /> </span><span>du</span><span>&nbsp;&mdash; show directory space usage</span><span><br /> </span><span>free</span><span>&nbsp;&mdash; show memory and swap usage</span><span><br /> </span><span>whereis app</span><span>&nbsp;&mdash; show possible locations of app</span><span><br /> </span><span>which app</span><span>&nbsp;&mdash; show which app will be run by default</span><span><br /> </span></li>
<li><span></span><span><strong>Process Management</strong></span><span><strong><br /> </strong></span><span>ps</span><span>&nbsp;&mdash; display your currently active processes</span><span><br /> </span><span>top</span><span>&nbsp;&mdash; display all running processes</span><span><br /> </span><span>kill pid</span><span>&nbsp;&mdash; kill process id pid</span><span><br /> </span><span>kill -9 pid</span><span>&nbsp;&mdash; force kill process id pid</span><span><br /> </span></li>
<li><span></span><span><strong>Permissions</strong></span><span><strong><br /> </strong></span><span>ls -l</span><span>&nbsp;&mdash; list items in current directory and show permissions</span><span><br /> </span><span>chmod ugo file</span><span>&nbsp;&mdash; change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.</span><span><br /> </span><span>7</span><span>&nbsp;&mdash; full permissions</span><span><br /> </span><span>6</span><span>&nbsp;&mdash; read and write only</span><span><br /> </span><span>5</span><span>&nbsp;&mdash; read and execute only</span><span><br /> </span><span>4</span><span>&nbsp;&mdash; read only</span><span><br /> </span><span>3</span><span>&nbsp;&mdash; write and execute only</span><span><br /> </span><span>2</span><span>&nbsp;&mdash; write only</span><span><br /> </span><span>1</span><span>&nbsp;&mdash; execute only</span><span><br /> </span><span>0</span><span>&nbsp;&mdash; no permissions</span><span><br /> </span><span>chmod 600 file</span><span>&nbsp;&mdash; you can read and write - good for files</span><span><br /> </span><span>chmod 700 file</span><span>&nbsp;&mdash; you can read, write, and execute - good for scripts</span><span><br /> </span><span>chmod 644 file</span><span>&nbsp;&mdash; you can read and write, and everyone else can only read - good for web pages</span><span><br /> </span><span>chmod 755 file</span><span>&nbsp;&mdash; you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share</span><span><br /> </span></li>
<li><span></span><span><strong>Networking</strong></span><span><strong><br /> </strong></span><span>wget file</span><span>&nbsp;&mdash; download a file</span><span><br /> </span><span>curl file</span><span>&nbsp;&mdash; download a file</span><span><br /> </span><span>scp user@host:file dir</span><span>&nbsp;&mdash; secure copy a file from remote server to the dir directory on your machine</span><span><br /> </span><span>scp file user@host:dir</span><span>&nbsp;&mdash; secure copy a file from your machine to the dir directory on a remote server</span><span><br /> </span><span>scp -r user@host:dir dir</span><span>&nbsp;&mdash; secure copy the directory dir from remote server to the directory dir on your machine</span><span><br /> </span><span>ssh user@host</span><span>&nbsp;&mdash; connect to host as user</span><span><br /> </span><span>ssh -p port user@host</span><span>&nbsp;&mdash; connect to host on port as user</span><span><br /> </span><span>ssh-copy-id user@host</span><span>&nbsp;&mdash; add your key to host for user to enable a keyed or passwordless login</span><span><br /> </span><span>ping host</span><span>&nbsp;&mdash; ping host and output results</span><span><br /> </span><span>whois domain</span><span>&nbsp;&mdash; get information for domain</span><span><br /> </span><span>dig domain</span><span>&nbsp;&mdash; get DNS information for domain</span><span><br /> </span><span>dig -x host</span><span>&nbsp;&mdash; reverse lookup host</span><span><br /> </span><span>lsof -i tcp:1337</span><span>&nbsp;&mdash; list all processes running on port 1337</span><span><br /> </span></li>
<li><span></span><span><strong>Searching</strong></span><span><strong><br /> </strong></span><span>grep pattern files</span><span>&nbsp;&mdash; search for pattern in files</span><span><br /> </span><span>grep -r pattern dir</span><span>&nbsp;&mdash; search recursively for pattern in dir</span><span><br /> </span><span>grep -rn pattern dir</span><span>&nbsp;&mdash; search recursively for pattern in dir and show the line number found</span><span><br /> </span><span>grep -r pattern dir --include='*.ext</span><span>&nbsp;&mdash; search recursively for pattern in dir and only search in files with .ext extension</span><span><br /> </span><span>command | grep pattern</span><span>&nbsp;&mdash; search for pattern in the output of command</span><span><br /> </span><span>find file</span><span>&nbsp;&mdash; find all instances of file in real system</span><span><br /> </span><span>locate file</span><span>&nbsp;&mdash; find all instances of file using indexed database built from the updatedb command. Much faster than find</span><span><br /> </span><span>sed -i 's/day/night/g' file</span><span>&nbsp;&mdash; find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions</span><span><br /> </span></li>
<li><span></span><span><strong>Compression</strong></span><span><strong><br /> </strong></span><span>tar cf file.tar files</span><span>&nbsp;&mdash; create a tar named file.tar containing files</span><span><br /> </span><span>tar xf file.tar</span><span>&nbsp;&mdash; extract the files from file.tar</span><span><br /> </span><span>tar czf file.tar.gz files</span><span>&nbsp;&mdash; create a tar with Gzip compression</span><span><br /> </span><span>tar xzf file.tar.gz</span><span>&nbsp;&mdash; extract a tar using Gzip</span><span><br /> </span><span>gzip file</span><span>&nbsp;&mdash; compresses file and renames it to file.gz</span><span><br /> </span><span>gzip -d file.gz</span><span>&nbsp;&mdash; decompresses file.gz back to file</span><span><br /> </span></li>
<li><span></span><span><strong>Shortcuts</strong></span><span><strong><br /> </strong></span><span>ctrl+a</span><span>&nbsp;&mdash; move cursor to beginning of line</span><span><br /> </span><span>ctrl+f</span><span>&nbsp;&mdash; move cursor to end of line</span><span><br /> </span><span>alt+f</span><span>&nbsp;&mdash; move cursor forward 1 word</span><span><br /> </span><span>alt+b</span><span>&nbsp;&mdash; move cursor backward 1 word</span><span><br /> </span></li>
<li></li>
</ul>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf</guid>
  <pubDate>Sun, 16 Feb 2020 02:57:40 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]></title>
  <description><![CDATA[
<p>https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html<br />Your profile:<br />Degree in bioinformatics, biostatistics, or equivalent<br />Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing<br />Strong competence in working in Unix/Linux environments (shell)<br />Strong programming skills (in particular: Python, R, Perl)<br />Experience with using git and snakemake<br />Fluent English language skills, both spoken and written<br />Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team</p>

<p>Additional Information:</p>

<p>If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).</p>

<p>Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).</p>

<p>Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.</p>

<p>Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/42003/perl-one-liner-for-beginners</guid>
	<pubDate>Fri, 24 Jul 2020 05:58:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/42003/perl-one-liner-for-beginners</link>
	<title><![CDATA[Perl one-liner for beginners !]]></title>
	<description><![CDATA[<p>I often use the following arguments to perl:</p><ul>
<li>-e Makes the line of code be executed instead of a script</li>
<li>-n Forces your line to be called in a loop. Allows you to take lines from the diamond operator (or stdin)</li>
<li>-p Forces your line to be called in a loop. Prints $_ at the end</li>
</ul><p>&nbsp;</p><ul>
<li>This counts the number of quotation marks in each line and prints it
<div>
<blockquote>
<div>perl -ne&nbsp;'$cnt = tr/"//;print "$cnt\n"'&nbsp;inputFileName.txt</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>Adds string to each line, followed by tab
<div>
<blockquote>
<div>perl -pe&nbsp;'s/(.*)/string\t$1/'&nbsp;inFile &gt; outFile</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>Append a new line to each line
<div>
<blockquote>
<div>perl -pe&nbsp;'s//\n/'&nbsp;all.sent.classOnly &gt; all.sent.classOnly.sep</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>Replace all occurrences of pattern1 (e.g. [0-9]) with pattern2
<div>
<blockquote>
<div>perl -p -i.bak -w -e&nbsp;'s/pattern1/pattern2/g'&nbsp;inputFile</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>Go through file and only print words that do not have any uppercase letters.
<div>
<blockquote>
<div>perl -ne&nbsp;'print unless m/[A-Z]/'&nbsp;allWords.txt &gt; allWordsOnlyLowercase.txt</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>Go through file, split line at each space and print words one per line.
<div>
<blockquote>
<div>perl -ne&nbsp;'print join("\n", split(/ /,$_));print("\n")'&nbsp;someText.txt &gt; wordsPerLine.txt</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>or in other words, delete every character that is not a letter, white space or line end (replace with nothing)
<div>
<blockquote>
<div>perl -pne&nbsp;'s/[^a-zA-Z\s]*//g'&nbsp;text_withSpecial.txt &gt; text_lettersOnly.txt</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>
<div>
<div>perl -pne&nbsp;'tr/[A-Z]/[a-z]/'&nbsp;textWithUpperCase.txt &gt; textwithoutuppercase.txt;</div>
</div>
</li>
</ul><ul>
<li>Print only the second column of the data when using tabular as a separator
<div>
<blockquote>
<div>perl -ne&nbsp;'@F = split("\t", $_); print "$F[1]";'&nbsp;columnFileWithTabs.txt &gt; justSecondColumn.txt</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>
<div>One-Liner: Sort lines by their length
<blockquote>
<div>perl -e&nbsp;'print sort {length $a &lt;=&gt; length $b} &lt;&gt;'&nbsp;textFile</div>
</blockquote>
</div>
</li>
</ul><ul>
<li>One-Liner: Print second column, unless it contains a number
<blockquote>
<div>perl"&gt;perl -lane&nbsp;'print $F[1] unless $F[1] =~ m/[0-9]/'&nbsp;wordCounts.txt</div>
</blockquote>
</li>
</ul>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43587/fix-rewritable-error-of-elgg</guid>
	<pubDate>Mon, 15 Nov 2021 06:23:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43587/fix-rewritable-error-of-elgg</link>
	<title><![CDATA[Fix rewritable error of ELGG !]]></title>
	<description><![CDATA[<p>The&nbsp;<code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;module uses a rule-based rewriting engine, based on a PCRE regular-expression parser, to rewrite requested URLs on the fly. By default,&nbsp;<code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;maps a URL to a filesystem path. However, it can also be used to redirect one URL to another URL, or to invoke an internal proxy fetch.</p>
<p><code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;provides a flexible and powerful way to manipulate URLs using an unlimited number of rules. Each rule can have an unlimited number of attached rule conditions, to allow you to rewrite URL based on server variables, environment variables, HTTP headers, or time stamps.</p>
<p><code><a href="https://httpd.apache.org/docs/2.4/mod/mod_rewrite.html">mod_rewrite</a></code>&nbsp;operates on the full URL path, including the path-info section. A rewrite rule can be invoked in&nbsp;<code>httpd.conf</code>&nbsp;or in&nbsp;<code>.htaccess</code>. The path generated by a rewrite rule can include a query string, or can lead to internal sub-processing, external request redirection, or internal proxy throughput.</p>
<p>Further details, discussion, and examples, are provided in the&nbsp;<a href="https://httpd.apache.org/docs/2.4/rewrite/">detailed mod_rewrite documentation</a>.</p>
<p>&nbsp;</p>
<ul>
<li>sudo a2enmod rewrite</li>
</ul>
<ul>
<li>sudo systemctl restart apache2</li>
</ul>
<ul>
<li>sudo nano /etc/apache2/sites-available/000-default.conf</li>
</ul>
<p>Write this</p>
<div title="/etc/apache2/sites-available/000-default.conf">/etc/apache2/sites-available/000-default.conf</div>
<div>
<div>
<pre><code><span>&lt;</span>VirtualHost *:8<span><span>0</span>&gt;</span>
    <span></span><span><span>&lt;</span>Directory /var/www/html<span>&gt;</span></span><span></span>
        <span>Options Indexes FollowSymLinks MultiViews</span>
        <span>AllowOverride All</span>
        <span>Require all granted</span>
    <span></span><span><span>&lt;</span>/Directory<span>&gt;</span></span><span></span>

    <span>.</span> <span>.</span> <span>.</span>
<span>&lt;</span>/VirtualHost<span>&gt;</span></code></pre>
</div>
</div><p>Address of the bookmark: <a href="https://www.digitalocean.com/community/tutorials/how-to-rewrite-urls-with-mod_rewrite-for-apache-on-ubuntu-18-04" rel="nofollow">https://www.digitalocean.com/community/tutorials/how-to-rewrite-urls-with-mod_rewrite-for-apache-on-ubuntu-18-04</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>

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