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<channel>
	<title>cygwin &amp;laquo; WordPress.com Tag Feed</title>
	<link>http://en.wordpress.com/tag/cygwin/</link>
	<description>Feed of posts on WordPress.com tagged "cygwin"</description>
	<pubDate>Sat, 28 Nov 2009 11:18:21 +0000</pubDate>

	<generator>http://en.wordpress.com/tags/</generator>
	<language>en</language>

<item>
<title><![CDATA[Cygwin corruption of $Recycle.Bin in Vista]]></title>
<link>http://smnuman.wordpress.com/2009/11/27/cygwin-corruption-of-recycle-bin-in-vista/</link>
<pubDate>Fri, 27 Nov 2009 20:13:07 +0000</pubDate>
<dc:creator>Syed Muhammad Numan</dc:creator>
<guid>http://smnuman.wordpress.com/2009/11/27/cygwin-corruption-of-recycle-bin-in-vista/</guid>
<description><![CDATA[When installing Cygwin sometimes it corrupts the $Recycle.Bin folder with it&#8217;s permission sett]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>When installing Cygwin sometimes it corrupts the $Recycle.Bin folder with it&#8217;s permission setting somehow. That in turn makes problem in your Vista OS while operating through the explorer.</p>
<p>Work around through it is a bit tricky for Vista. Here is what you can do :</p>
<p>
<blockquote><strong>Option #1</strong><br />
Restore to previous version the root drive</p></blockquote>
<p>Alternatively, if you can&#8217;t succeed doing that or do not have any option for doing that try the following:</p>
<p>
<blockquote><strong>Option #2</strong><br />
Start a command prompt or type <code><strong>cmd</strong></code> at the run prompt with admin rights.<br />
Type the followings:</p>
<pre><code>
cd \
attrib -S -H /S $Recycle.Bin
del /F /S /Q /ASH $Recycle.Bin\
exit
</code></pre>
</blockquote>
<p><strong>Helpful sites for non-vista users:</strong><br />
<a href="http://www.setup32.com/tech-tips/windows-nt/disk-and-file-management/fix-recycle-bin.php">Setup32.com</a><br />
<a href="http://support.microsoft.com/kb/297760">Microsoft support</a></p>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[Linux-like Environment for Windows]]></title>
<link>http://goloprak.wordpress.com/2009/11/27/me-remote-desktop-linux-di-windows/</link>
<pubDate>Fri, 27 Nov 2009 03:40:06 +0000</pubDate>
<dc:creator>Agus  RN</dc:creator>
<guid>http://goloprak.wordpress.com/2009/11/27/me-remote-desktop-linux-di-windows/</guid>
<description><![CDATA[Kalau anda ingin merasakan suasana linux di windows cobalah cygwin. Untuk keterangan lebih lanjut ku]]></description>
<content:encoded><![CDATA[Kalau anda ingin merasakan suasana linux di windows cobalah cygwin. Untuk keterangan lebih lanjut ku]]></content:encoded>
</item>
<item>
<title><![CDATA[Configuring proxy in Cygwin or Bash/Ubuntu]]></title>
<link>http://rafacastanho.wordpress.com/2009/11/25/configuring-proxy-in-cygwin/</link>
<pubDate>Wed, 25 Nov 2009 19:22:45 +0000</pubDate>
<dc:creator>Rafael Castanho</dc:creator>
<guid>http://rafacastanho.wordpress.com/2009/11/25/configuring-proxy-in-cygwin/</guid>
<description><![CDATA[Hi fellas!!! This week I pass through a pain in the ass &#8216;bug&#8217; to access internet through]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Hi fellas!!!</p>
<p>This week I pass through a <em><del datetime="2009-11-25T19:13:57+00:00">pain in the ass</del></em> &#8216;bug&#8217; to access internet through a proxy using my <a href="http://www.cygwin.com/">cygwin</a>.</p>
<p><strong>So, how to configure your cygwin to use your company proxy:</strong></p>
<pre class="brush: xml;">export http_proxy=http://DOMAIN\\USERNAME:PASSWORD@proxy.mycompany.com:8080</pre>
<p><em>Obs. </em>domain, username and passwd are option, check with your company</p>
<hr />
Important thing is to check witch type of auth your proxy support.<br />
We have some types of auth in proxys:</p>
<ul>
<li>Basic (plain text)</li>
<li>Digest</li>
<li>Integrate/NTLM</li>
<li>Radious</li>
</ul>
<p>And for example if your company did <strong>not</strong> support basic, you are <em>screwed</em> =P</p>
<p>Check my post in <a href="http://serverfault.com/questions/88263/configuring-proxy-terminal-ubuntu">ServerFault</a></p>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[cygwin: zsh: zsh compinit: insecure directories]]></title>
<link>http://soniahamilton.wordpress.com/2009/11/19/cygwin-zsh-zsh-compinit-insecure-directories/</link>
<pubDate>Thu, 19 Nov 2009 05:21:39 +0000</pubDate>
<dc:creator>Sonia</dc:creator>
<guid>http://soniahamilton.wordpress.com/2009/11/19/cygwin-zsh-zsh-compinit-insecure-directories/</guid>
<description><![CDATA[Using cygwin under Windows, I&#8217;ve setup my shell as zsh by editing the launch script: @echo off]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Using cygwin under Windows, I&#8217;ve setup my shell as zsh by editing the launch script:</p>
<pre>@echo off
C:
chdir C:\cygwin\bin
zsh -l -i
</pre>
<p>Unfortunately, this gives a nasty error everytime the shell is started up, due to Cygwin installing zsh incorrectly:</p>
<pre>zsh compinit: insecure directories, run compaudit for list.
Ignore insecure directories and continue [y] or abort compinit [n]? y</pre>
<p>Solution, thanks to <a href="http://www.wezm.net/2008/09/zsh-cygwin-and-insecure-directories/">wezm.net</a>:</p>
<pre>compaudit &#124; xargs chmod g-w</pre>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[Maven https repository with self-signed ssl certificate]]></title>
<link>http://ahoehma.wordpress.com/2009/11/17/maven-https-repository-with-self-signed-ssl-certificate/</link>
<pubDate>Tue, 17 Nov 2009 12:39:56 +0000</pubDate>
<dc:creator>Andreas Höhmann</dc:creator>
<guid>http://ahoehma.wordpress.com/2009/11/17/maven-https-repository-with-self-signed-ssl-certificate/</guid>
<description><![CDATA[For a private project I try to use nexus behind apache and ssl. I used a self-signed certificate. Bu]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>For a private project I try to use nexus behind apache and ssl. I used a self-signed certificate.</p>
<p>But each nexus repository request ends with a security exception:</p>
<p><code>[WARNING] repository metadata for: 'artifact org.apache.maven.plugins:maven-enforcer-plugin' could not be retrieved from repository: nexus-plugin-releases due to an error: Error transferring file: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target<br />
</code></p>
<p>I found many site for that problem and they describe always the same solution</p>
<p><strong>import the self signed cert in your local truststore!</strong></p>
<p>&#8230; here are the steps:</p>
<ol>
<li>download the certificate</li>
<li>create a local truststore and import the certificat</li>
<li>call maven with the correct security properties</li>
</ol>
<p>The import is simple  (java keytool):</p>
<pre>keytool.exe -importcert
            -alias nexus-xxx
            -keystore xxx.jks
            -storepass secret
            -file xxx.crt</pre>
<p>For maven I&#8217;m using a cygwin bash alias:</p>
<pre>alias mvn_xxx='/cygdrive/d/maven-2.2.1/bin/mvn
-gs "d:/maven-2.2.1/conf/settings-xxx.xml"
-s "d:/maven-2.2.1/conf/settings-xxx.xml"
-Djavax.net.ssl.trustStore=d:/maven-2.2.1/conf/xxx.jks
-Djavax.net.ssl.trustStorePassword=secret'</pre>
<p>I point the global config  (<em>-gs</em>) and the personal config (<em>-s</em>) to the same file to ignore other configuration from my default maven config file (i.e. common mirros settings / repositories etc.).</p>
<p>And at least here is my complete maven setting-nexus settings:</p>
<pre class="brush: xml;">
&#60;?xml version=&#34;1.0&#34; encoding=&#34;UTF-8&#34;?&#62;
&#60;settings xmlns=&#34;http://maven.apache.org/settings/1.0.0&#34; xmlns:xsi=&#34;http://www.w3.org/2001/XMLSchema-instance&#34;
  xsi:schemaLocation=&#34;http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd&#34;&#62;

  &#60;localRepository&#62;D:\maven-repository-xxx&#60;/localRepository&#62;

  &#60;mirrors&#62;
    &#60;mirror&#62;
      &#60;id&#62;xxx-nexus-snapshots&#60;/id&#62;
      &#60;mirrorOf&#62;nexus-snapshots&#60;/mirrorOf&#62;
      &#60;url&#62;https://nexus.xxx.com/content/groups/public-snapshots/&#60;/url&#62;
    &#60;/mirror&#62;
    &#60;mirror&#62;
      &#60;id&#62;xxx-nexus-snapshots&#60;/id&#62;
      &#60;mirrorOf&#62;nexus-plugin-snapshots&#60;/mirrorOf&#62;
      &#60;url&#62;https://nexus.xxx.com/content/groups/public-snapshots/&#60;/url&#62;
    &#60;/mirror&#62;
    &#60;mirror&#62;
      &#60;id&#62;xxx-nexus-releases&#60;/id&#62;
      &#60;mirrorOf&#62;nexus-releases&#60;/mirrorOf&#62;
      &#60;url&#62;https://nexus.xxx.com/content/groups/public/&#60;/url&#62;
    &#60;/mirror&#62;
    &#60;mirror&#62;
      &#60;id&#62;xxx-nexus-releases&#60;/id&#62;
      &#60;mirrorOf&#62;nexus-plugin-releases&#60;/mirrorOf&#62;
      &#60;url&#62;https://nexus.xxx.com/content/groups/public/&#60;/url&#62;
    &#60;/mirror&#62;
    &#60;mirror&#62;
      &#60;id&#62;xxx-nexus-releases&#60;/id&#62;
      &#60;mirrorOf&#62;*&#60;/mirrorOf&#62;
      &#60;url&#62;https://nexus.xxx.com/content/groups/public/&#60;/url&#62;
    &#60;/mirror&#62;
  &#60;/mirrors&#62;

  &#60;profiles&#62;
    &#60;profile&#62;
      &#60;id&#62;xxx-nexus-mirror&#60;/id&#62;
      &#60;activation&#62;
        &#60;activeByDefault&#62;true&#60;/activeByDefault&#62;
      &#60;/activation&#62;
      &#60;repositories&#62;
        &#60;repository&#62;
          &#60;id&#62;nexus-releases&#60;/id&#62;
          &#60;url&#62;http://foobar&#60;/url&#62;
          &#60;releases&#62;
            &#60;enabled&#62;true&#60;/enabled&#62;
          &#60;/releases&#62;
          &#60;snapshots&#62;
            &#60;enabled&#62;false&#60;/enabled&#62;
          &#60;/snapshots&#62;
        &#60;/repository&#62;
        &#60;repository&#62;
          &#60;id&#62;nexus-snapshots&#60;/id&#62;
          &#60;url&#62;http://foobar&#60;/url&#62;
          &#60;releases&#62;
            &#60;enabled&#62;false&#60;/enabled&#62;
          &#60;/releases&#62;
          &#60;snapshots&#62;
            &#60;enabled&#62;true&#60;/enabled&#62;
          &#60;/snapshots&#62;
        &#60;/repository&#62;
      &#60;/repositories&#62;
      &#60;pluginRepositories&#62;
        &#60;pluginRepository&#62;
          &#60;id&#62;nexus-plugin-releases&#60;/id&#62;
          &#60;url&#62;http://foobar&#60;/url&#62;
          &#60;releases&#62;
            &#60;enabled&#62;true&#60;/enabled&#62;
          &#60;/releases&#62;
          &#60;snapshots&#62;
            &#60;enabled&#62;false&#60;/enabled&#62;
          &#60;/snapshots&#62;
        &#60;/pluginRepository&#62;
        &#60;pluginRepository&#62;
          &#60;id&#62;nexus-plugin-snapshots&#60;/id&#62;
          &#60;url&#62;http://foobar&#60;/url&#62;
          &#60;releases&#62;
            &#60;enabled&#62;false&#60;/enabled&#62;
          &#60;/releases&#62;
          &#60;snapshots&#62;
            &#60;enabled&#62;true&#60;/enabled&#62;
          &#60;/snapshots&#62;
        &#60;/pluginRepository&#62;
      &#60;/pluginRepositories&#62;
    &#60;/profile&#62;
  &#60;/profiles&#62;

  &#60;servers&#62;
    &#60;server&#62;
      &#60;id&#62;xxx-nexus-releases&#60;/id&#62;
      &#60;username&#62;foo&#60;/username&#62;
      &#60;password&#62;bar&#60;/password&#62;
    &#60;/server&#62;
    &#60;server&#62;
      &#60;id&#62;xxx-nexus-snapshots&#60;/id&#62;
      &#60;username&#62;foo&#60;/username&#62;
      &#60;password&#62;bar&#60;/password&#62;
    &#60;/server&#62;
  &#60;/servers&#62;

&#60;/settings&#62;
</pre>
<p>You can replace xxx with your personal domain-alias.</p>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[Cygwin]]></title>
<link>http://zuzeme.wordpress.com/2009/11/10/cygwin/</link>
<pubDate>Tue, 10 Nov 2009 17:50:54 +0000</pubDate>
<dc:creator>zuzoa</dc:creator>
<guid>http://zuzeme.wordpress.com/2009/11/10/cygwin/</guid>
<description><![CDATA[I&#8217;ve installed it again, with a purpose this time. I want to move this giant 6GB iso file over]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>I&#8217;ve installed it again, with a purpose this time. I want to move this giant 6GB iso file over to my external to make space, but of course the external is FAT32 and can&#8217;t handle that file size. So, in linux, I would simply split the file into smaller chunks with `split`, to be reassembled with `cat` later, but&#8230; What am I supposed to in Windows? Download some shady file-splitting software? No thanks.</p>
<p>Well, to my satisfaction, I am now successfully splitting the file with `split` under cygwin. Cygwin has proved it&#8217;s potential and usefulness to me, so I will give it another try. <img src='http://s.wordpress.com/wp-includes/images/smilies/icon_wink.gif' alt=';)' class='wp-smiley' /> </p>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[Cscope + Notepad++ Coding nirvana!]]></title>
<link>http://allajunaki.wordpress.com/2009/11/10/cscope-notepad-coding-nirvana/</link>
<pubDate>Tue, 10 Nov 2009 14:46:06 +0000</pubDate>
<dc:creator>allajunaki</dc:creator>
<guid>http://allajunaki.wordpress.com/2009/11/10/cscope-notepad-coding-nirvana/</guid>
<description><![CDATA[Loved Cscope on cygwin, but hated the fact that you anything you select will open up in Vi, and then]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Loved Cscope on cygwin, but hated the fact that you anything you select will open up in Vi, and then do some keyboard voodoo to get back to the cscope window?</p>
<p>Or are you one of those fan of notepad++ awesomeness but love the way cscope hunts for stuff for ya?</p>
<p>Fear not, there is a way both your sweethearts can now play with you, all at the same time for an awesome threesome <img src='http://s.wordpress.com/wp-includes/images/smilies/icon_wink.gif' alt=';)' class='wp-smiley' /> </p>
<p>Just export these lines before you fire up Cscope</p>
<pre>export CSCOPE_EDITOR="/cygdrive/c/Program Files/Notepad++/notepad++.exe"
export CSCOPE_LINEFLAG="-n%s"
</pre>
<p>Please note : Change the CSCOPE_EDITOR path to where your notepad++ is currently residing. For your convenience, I have included the path that is default for Normal install of notepad++.</p>
<p>Better still, put it in a script file (or perhaps bashrc).</p>
<p>Got a better suggestion? Post a comment <img src='http://s.wordpress.com/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[using keychain under cygwin]]></title>
<link>http://thomaswabner.wordpress.com/2009/11/06/using-keychain-under-cygwin/</link>
<pubDate>Fri, 06 Nov 2009 13:39:31 +0000</pubDate>
<dc:creator>Thomas Wabner</dc:creator>
<guid>http://thomaswabner.wordpress.com/2009/11/06/using-keychain-under-cygwin/</guid>
<description><![CDATA[If you want to use the keychain tool under cygwin to aviod entering your passwort for your external ]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>If you want to use the <a href="http://www.gentoo.org/proj/en/keychain/">keychain</a> tool under <a href="http://www.cygwin.com/">cygwin</a> to aviod entering your passwort for your external server again and agin, you may follow my short guide:</p>
<p>In the follow example I work on my home PC named <em>master</em> and want to use the keychain tool with my server <em>test-server.de</em>.</p>
<ol>
<li>Install the <a href="http://www.gentoo.org/proj/en/keychain/">keychain</a> tool under <a href="http://www.cygwin.com/">cygwin</a></li>
<li>Start you cygwin bash and generate your own private and public key pair:
<pre class="brush: bash;">
ssh-keygen
</pre>
<p>Of course you should set a password for your private key. The keys are now in $HOME/.ssh/</li>
<li>Copy your public key from $HOME/.ssh/id_rsa.pub to your <em>test-server.de</em> (in a temporary folder)</li>
<li>Login to your <em>test-server.de</em></li>
<li>Copy the content of your public key and insert it at the end of your $HOME/.ssh/known_host. If the file does not exists, create a new one.</li>
<li>Logout from your <em>test-server.de</em></li>
<li>Now you can do the following <strong>every time</strong> you start your cygwin shell:</li>
<li>Start the keychain tool with your private key:
<pre class="brush: bash;">
/usr/bin/keychain $HOME/.ssh/id_rsa
</pre>
</li>
<li>Source the generated sh file from keychain:
<pre class="brush: bash;">
source $HOME/.keychain/master-sh
</pre>
<p>Dependend of your hostname (in my example master) the file name from the keychain directory may differ.
</li>
</ol>
<p>To stop the ssh-agent (which is started in the background from the keychain tool) you may use</p>
<pre class="brush: bash;">
keychain -k all
</pre>
<p>If you have more than one server where you want to connect without retyping the password you can re run <strong>steps 3-6</strong> from the guide.</p>
</div>]]></content:encoded>
</item>
<item>
<title><![CDATA[Linux like development environment in Windows]]></title>
<link>http://prajwalaa.wordpress.com/2009/11/06/linux-like-development-environment-in-windows/</link>
<pubDate>Thu, 05 Nov 2009 18:35:07 +0000</pubDate>
<dc:creator>Prajwala</dc:creator>
<guid>http://prajwalaa.wordpress.com/2009/11/06/linux-like-development-environment-in-windows/</guid>
<description><![CDATA[I am a fan of Linux based OS. I love Ubuntu a lot. In fact I started my programming in Redhat. So fr]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><div style="line-height:1.4em;font-family:georgia;font-size:16px;">
<p>I am a fan of Linux based OS. I love Ubuntu a lot. In fact I started my programming in Redhat. So from the beginning I am comfortable using Linux than Windows. The only reason I use windows is to check IE browser compatability.</p>
<p>Recently I attended Drupal Sprint India 2009. I want to attend the sprint, so I need one Laptop to go there and work. My company provided me Laptop with Windows. So I need to work on drupal core issues in windows. Hmm it looks very hard for me to work in Windows. I want to have following things in my Windows machine.</p>
<ol>
<li> Cygwin to get the linux like terminal, so that I can see paths with forward slash.</li>
<li> Xampp Lite to get Apache, Mysql, PHP.</li>
<li>cvs, I am going to work on drupal core so I need it</li>
<li>I should able to create patches, apply patches.</li>
<li>I want to use Drupal Drush module, which provides some command line utilities</li>
<li>Emacs. I am more comfortable with this editor. It is very hard to work with other editors once we are comfortable with Emacs</li>
</ol>
<p>First I installed the things I know like Cygwin, Xampp Lite.</p>
<p><strong>Installing Emacs</strong></p>
<p>I Installed Emacs by following instructions at <a href="http://www.claremontmckenna.edu/math/ALee/emacs/emacs.html" target="_blank">http://www.claremontmckenna.edu/math/ALee/emacs/emacs.html</a> .</p>
<p><strong>Installing UnxUtils</strong></p>
<p>To be able create patches and apply patches I installed unxutils from <a href="http://sourceforge.net/projects/unxutils/" target="_blank">http://sourceforge.net/projects/unxutils/</a> . With this unxutils I got most of the Linux commands. The commands like ls, mkdir, wget, diff, patch, tar, zip etc&#8230; are working. I am very happy after installing unixutils.<br />
Installing UnxUtils is nothing but setting the path variable in Windows. I extracted the unixutils directory in C folder and Add C:\unixutils\usr\local\wbin path to the Path variable. In Windows XP we can set the Path variable by going to control panel &#62; System &#62; Advanced &#62; Environment Variables. Select the Path and click Edit and add your path to the existing path.</p>
<p><strong>Installing Drush</strong></p>
<p>There is a documentation about installing Drush in Windows <a href="http://drupal.org/node/594744" target="_blank">http://drupal.org/node/594744</a> . This document explain Drush installation by using GnuWin32. But I already installed UnxUtils so I don&#8217;t require GnuWin32. So first 3 steps in the <a href="http://drupal.org/node/594744" target="_blank">http://drupal.org/node/594744</a> can be ignored. I extracted drush in C folder. As specified in the step 4 of <a href="http://drupal.org/node/594744" target="_blank">http://drupal.org/node/594744</a> I edited drush.bat with the path of php.exe and path of drush.php. I added following statement in drush.bat file<br />
<code> @E:\xampplite\php\php.exe C:\drush\drush.php %1 %2 %3 %4 %5 %6 %7 %8 %9 </code></p>
<p>Because I used xampplite to install php, php is there at path E:\xampplite\php\php.exe.Now I executed drush command from the windows terminal by specifying -r and -l attributes.<br />
After that I got an idea why can&#8217;t I keep this php, drush paths also in path so that I can directly drush.bat file as it is. Yes I added php, drush, mysql paths in Windows Path variable. The everything works file.</p>
<p><strong>Installing cvs</strong></p>
<p>I downloaded TortoiseCVS from <a href="http://www.tortoisecvs.org/download.shtml" target="_blank">http://www.tortoisecvs.org/download.shtml</a>. This is a exe file, I can simple double click and execute.</p>
<p>That&#8217;s it, Now I installed all the things necessary to work on drupal with a linux like environment. Now I am happy to work on windows.</p>
</div>
</div>]]></content:encoded>
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<title><![CDATA[QuickTip: Running Java with Classpath in Cygwin]]></title>
<link>http://svashishtha.wordpress.com/2009/11/04/quick-tip-running-java-with-classpath-in-cygwin/</link>
<pubDate>Wed, 04 Nov 2009 12:05:26 +0000</pubDate>
<dc:creator>ShriKant Vashishtha</dc:creator>
<guid>http://svashishtha.wordpress.com/2009/11/04/quick-tip-running-java-with-classpath-in-cygwin/</guid>
<description><![CDATA[If you are running a Java program and your classpath is in UNIX separator style (&#8216;/&#8217; ins]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>If you are running a Java program and your classpath is in UNIX separator style (&#8216;/&#8217; instead of &#8216;\&#8217;), you may be in trouble as java.exe is Windows specific executable which understands Windows separator and not UNIX style separator. To circumvent this issue in your shell script you can use the following:<br />
<code><br />
java -cp `cygpath -wp $CLASSPATH`<br />
</code></p>
<p>instead of </p>
<p><code><br />
java -cp $CLASSPATH<br />
</code></p>
</div>]]></content:encoded>
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<title><![CDATA[Toggle jrebel with a cygwin bash function and maven]]></title>
<link>http://ahoehma.wordpress.com/2009/11/02/toogle-jrebel-with-a-cygwin-bash-function-and-maven/</link>
<pubDate>Mon, 02 Nov 2009 13:57:16 +0000</pubDate>
<dc:creator>Andreas Höhmann</dc:creator>
<guid>http://ahoehma.wordpress.com/2009/11/02/toogle-jrebel-with-a-cygwin-bash-function-and-maven/</guid>
<description><![CDATA[I&#8217;m using java rebel for web development with maven. Sometimes I would run jetty with jrebel s]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>I&#8217;m using <a href="http://www.zeroturnaround.com/jrebel/" target="_blank">java rebel</a> for web development with maven.</p>
<p>Sometimes I would run jetty with jrebel sometimes without.</p>
<p>For that I&#8217;m using two simple bash functions:</p>
<pre class="brush: bash;">
# ~/.bashrc

#
# Maven options
#
export INTERNAL_MAVEN_OPTS=&#34;-Xmx512m -XX:PermSize=128m -XX:MaxPermSize=128m&#34;

#
# Java Rebel
#
export JAVA_REBEL=&#34;-Drebel.spring_plugin=true -Drebel.log=false -noverify -javaagent:D:\tools\javarebel\jrebel.jar -Drebel.packages=de.ahoehma&#34;

function jrebel_on() {
 export MAVEN_OPTS=&#34;$INTERNAL_MAVEN_OPTS $JAVA_REBEL&#34;
}

function jrebel_off() {
 export MAVEN_OPTS=&#34;$INTERNAL_MAVEN_OPTS&#34;
}
</pre>
<p>Now its very simple to enable</p>
<pre class="brush: bash;">
$ jrebel_on
</pre>
<p>or disable jrebel</p>
<pre class="brush: bash;">
$ jrebel_off
</pre>
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<title><![CDATA[Docking Molekuler dengan Autodock di Windows]]></title>
<link>http://abuumar80.wordpress.com/2009/10/30/running-autodock-di-windows/</link>
<pubDate>Fri, 30 Oct 2009 09:09:52 +0000</pubDate>
<dc:creator>abuumar80</dc:creator>
<guid>http://abuumar80.wordpress.com/2009/10/30/running-autodock-di-windows/</guid>
<description><![CDATA[Autodock merupakan aplikasi yang populer digunakan saat ini dalam studi docking molekuler. Software ]]></description>
<content:encoded><![CDATA[Autodock merupakan aplikasi yang populer digunakan saat ini dalam studi docking molekuler. Software ]]></content:encoded>
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<title><![CDATA[Grepping lines with multiple matches]]></title>
<link>http://benbiddington.wordpress.com/2009/10/23/grepping-lines-with-multiple-matches/</link>
<pubDate>Fri, 23 Oct 2009 12:37:55 +0000</pubDate>
<dc:creator>benbiddington</dc:creator>
<guid>http://benbiddington.wordpress.com/2009/10/23/grepping-lines-with-multiple-matches/</guid>
<description><![CDATA[I want to filter log files by matching lines that contains all of  set of matches (I don&#8217;t wan]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>I want to filter log files by matching lines that contains all of  set of matches (I don&#8217;t want to alternate them).</p>
<p>For example lines like:</p>
<pre style="padding-left:30px;">RawURL /1.2/user/authorize?ip=10.254.142.175&#38;method=GET</pre>
<p>I want to match lines that contain the terms &#8220;RawURL&#8221; and &#8220;/1.2/user/authorize?&#8221; without resorting to piping multiple greps:</p>
<pre style="padding-left:30px;">$ grep RawURL &#124; grep /1.2/user/authorize? *.txt</pre>
<p>This means I want a regexp like:</p>
<pre style="padding-left:30px;">RawURL.+\/1.2\/user\/authorize</pre>
<p>Translating to grep extended regex, this becomes:</p>
<pre style="padding-left:30px;">$ grep -E RawURL.+/1.2/user/authorize *.txt</pre>
<p>Note: There is no need to enforce non-greedy matching.</p>
<h3>Regular expressions, character classes and special characters</h3>
<p>The expression:</p>
<pre style="font:normal normal normal 12px/18px Consolas, Monaco, 'Courier New', Courier, monospace;padding-left:30px;">RawURL.+\/1.2\/user\/authorize</pre>
<p>Is not equivalent to:</p>
<pre style="padding-left:30px;">RawURL[.]+\/1.2\/user\/authorize</pre>
<p>Because in the second one, the special character &#8216;.&#8217; is no longer special. <a href="http://www.regular-expressions.info/charclass.html" target="_blank">Character classes</a> have all special characters turned off.</p>
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<title><![CDATA[Working with Cygterm on Windows]]></title>
<link>http://svashishtha.wordpress.com/2009/10/11/working-with-cygterm-on-windows/</link>
<pubDate>Sun, 11 Oct 2009 06:54:56 +0000</pubDate>
<dc:creator>ShriKant Vashishtha</dc:creator>
<guid>http://svashishtha.wordpress.com/2009/10/11/working-with-cygterm-on-windows/</guid>
<description><![CDATA[Quite a few of my colleagues use Ubuntu as OS for development purposes. For all these years, though ]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Quite a few of my colleagues use Ubuntu as OS for development purposes. For all these years, though I have been working on Linux and UNIX, I haven&#8217;t migrated to full-fledged Linux because of many reasons. As working with command line provides a lot of efficiency I use cygwin. However though cygwin works with DOS based &#8220;cmd&#8221;, I never liked using &#8220;cmd&#8221; in all these years just because it doesn&#8217;t look good compared to putty or similar softwares. With quite a few research I found puttycyg which is a putty extension of cygwin. For this to work, you should already have cygwin installed. After downloading it from http://code.google.com/p/puttycyg/ you need to create a shortcut on your desktop with following target:<br />
<code><br />
$PATH_TO_PUTTYCYG\puttycyg-20090811\putty.exe -cygterm -<br />
</code></p>
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<title><![CDATA[An Easy Introduction to C++ in Windows]]></title>
<link>http://twofoldgaze.wordpress.com/2009/10/06/an-easy-introduction-to-c-in-windows/</link>
<pubDate>Tue, 06 Oct 2009 21:25:58 +0000</pubDate>
<dc:creator>Kareem Carr</dc:creator>
<guid>http://twofoldgaze.wordpress.com/2009/10/06/an-easy-introduction-to-c-in-windows/</guid>
<description><![CDATA[An easy way to get started with C++ on a Windows system is to install Cygwin. Here is a detailed gui]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>An easy way to get started with C++ on a Windows system is to install <a href="http://www.cygwin.com/">Cygwin</a>.  Here is a detailed guide to installing Cygwin.</p>
<p><!--more-->1. Go the <a href="http://www.cygwin.com/">Cygwin site</a> and download the setup.exe file by clicking on the icon with the green center and the black border.</p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin01.png"><img class="aligncenter size-full wp-image-430" title="Cygwin0" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin01.png" alt="Cygwin0" width="505" height="282" /></a></p>
<p>2.<strong>Cygwin Net Release Setup Program:</strong> Click <em>Next</em></p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin1.png"><img class="aligncenter size-full wp-image-413" title="Cygwin1" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin1.png" alt="Cygwin1" width="511" height="397" /></a></p>
<p>3. <strong>Choose A Download Source:</strong> Select <em>Install from Internet</em> and click <em>Next</em></p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin2.png"><img class="aligncenter size-full wp-image-414" title="Cygwin2" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin2.png" alt="Cygwin2" width="512" height="395" /></a></p>
<p>4. <strong>Select Root Install Directory:</strong> I would suggest accepting the defaults for this page and clicking <em>Next</em></p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin3.png"><img class="aligncenter size-full wp-image-415" title="Cygwin3" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin3.png" alt="Cygwin3" width="516" height="398" /></a></p>
<p>5. <strong>Select Local Package Directory:</strong> This is where the installation files are stored.  In the picture below, there is blank because this line is specific to how you&#8217;ve set up your computer.  You should see a directory on your screen.  It&#8217;s okay to accept the default that the cygwin installer provides and to click <em>Next</em></p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin4.png"><img class="aligncenter size-full wp-image-420" title="Cygwin4" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin4.png" alt="Cygwin4" width="513" height="397" /></a></p>
<p>6. <strong>Select Your Internet Connection:</strong> Select <em>Direct Connection</em> and click <em>Next</em></p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin5.png"><img class="aligncenter size-full wp-image-416" title="Cygwin5" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin5.png" alt="Cygwin5" width="512" height="396" /></a></p>
<p>7. <strong>Choose A Download Site:</strong> This is a list of possible sources for downloading the code.  I usually pick a nearby university or government source. For instance, the anl.gov source is the Argonne National Laboratory and is a reasonable choice for someone in the Midwest.</p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin6.png"><img class="aligncenter size-full wp-image-418" title="Cygwin6" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin6.png" alt="Cygwin6" width="512" height="394" /></a></p>
<p>8. <strong>Select Packages:</strong> Here we have many possible choices.  However, we only need to make one selection to install C++.  Expand <em>Devel</em>.  Find the <em>gcc-g++: C++ compiler</em> entry in the <em>Package</em> column.  Click the corresponding entry in the <em>New</em> column which should say <em>Skip</em>.  <em>Skip</em> should now change to some numbers representing the most recent version of that package for Cygwin.  Now click <em>Next</em>.</p>
<p><a href="http://twofoldgaze.wordpress.com/files/2009/10/cygwin7.png"><img class="aligncenter size-full wp-image-419" title="Cygwin7" src="http://twofoldgaze.wordpress.com/files/2009/10/cygwin7.png" alt="Cygwin7" width="512" height="396" /></a></p>
<p>9. <strong>Progress:</strong>The program downloads and installs Cygwin.  This could take a while depending on your internet connection and your choice of download site.</p>
<p>10. <strong>Installation complete:</strong>Click <em>Finish</em></p>
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<title><![CDATA[Herramientas GNU en Windows]]></title>
<link>http://jinetedeldragon.wordpress.com/2009/09/30/herramientas-gnu-en-windows/</link>
<pubDate>Wed, 30 Sep 2009 18:35:09 +0000</pubDate>
<dc:creator>jinetedeldragon</dc:creator>
<guid>http://jinetedeldragon.wordpress.com/2009/09/30/herramientas-gnu-en-windows/</guid>
<description><![CDATA[Antes que nada, esto es una solución a la pésima consola (cmd.exe) que tiene Windows. En mi trabajo ]]></description>
<content:encoded><![CDATA[Antes que nada, esto es una solución a la pésima consola (cmd.exe) que tiene Windows. En mi trabajo ]]></content:encoded>
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<title><![CDATA[siteinfo.sh - shellscript för att kolla upp en domän]]></title>
<link>http://hex29a.wordpress.com/2009/09/25/siteinfo-sh-shellscript-for-att-kolla-upp-en-doman/</link>
<pubDate>Fri, 25 Sep 2009 09:41:20 +0000</pubDate>
<dc:creator>hex29a</dc:creator>
<guid>http://hex29a.wordpress.com/2009/09/25/siteinfo-sh-shellscript-for-att-kolla-upp-en-doman/</guid>
<description><![CDATA[Äntligen fredag! Detta firas idag av ett litet fulhack jag skrev för att snabbt dra fram lite info o]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Äntligen fredag! Detta firas idag av ett litet fulhack jag skrev för att snabbt dra fram lite info om en domän.</p>
<p>Det är som sagt ett fulhack och funkar inte särskilt bra om domänen är ett alias t.ex.</p>
<p>Scriptet börjar med att köra en förfrågan om domänen hos netcraft för att få fram vem som står som ägare till nätet där ipadressen finns.</p>
<p>Sedan körs en &#8216;host&#8217; för att få fram ip-adressen följt av en &#8216;dig -x&#8217; för att få reverse-dns adress. <em>(Många hemsidor ligger ju som vhostar hos olika webbhotell)</em></p>
<p>Här är ett exempel på output när scriptet körs mot &#8216;example.com&#8217;</p>
<blockquote><p>Network info for: example.com</p>
<p>IP:             208.77.188.166<br />
REVERSE:        www.example.com.<br />
NETBLOCK:       ICANN</p></blockquote>
<p>Scriptet är testat i OpenBSD, Ubuntu och i Cygwinmiljö och kan laddas ner <a title="siteinfo.sh" href="http://www.box.net/shared/sohps4ded6">här</a>.</p>
<p>För att köra siteinfo.sh behövs curl.</p>
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<title><![CDATA[Converter fontes .otf para .ttf]]></title>
<link>http://zoltral.wordpress.com/2009/09/11/converter-fontes-otf-para-ttf/</link>
<pubDate>Sat, 12 Sep 2009 01:17:21 +0000</pubDate>
<dc:creator>zoltral</dc:creator>
<guid>http://zoltral.wordpress.com/2009/09/11/converter-fontes-otf-para-ttf/</guid>
<description><![CDATA[Hoje eu estava procurando algumas fontes novas para um projeto pessoal que estou desenvolvendo. Enco]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Hoje eu estava procurando algumas fontes novas para um projeto pessoal que estou desenvolvendo.</p>
<p>Encontrei várias, mas me deparei com um problema. Algumas dessas fontes tem extensão .otf. Baixei elas, mas não consegui utilizar.</p>
<p>Pesquisei e descobri que o programa <a href="http://fontforge.sourceforge.net/">FontForge</a> converte essas fontes para .ttf, mas ainda ficou o problema de converter muitas fontes. Usando a interface gráfica do FontForge é muito demorado.</p>
<p>Mais um pouco de pesquisa e descobri um <a href="http://www.stuermer.ch/blog/convert-otf-to-ttf-font-on-ubuntu.html">pequeno script</a> que resolve mais este problema.</p>
<p>Segue o script:</p>
<p><code>#!/usr/local/bin/fontforge<br />
# Quick and dirty hack: converts a font to truetype (.ttf)<br />
Print("Opening "+$1);<br />
Open($1);<br />
Print("Saving "+$1:r+".ttf");<br />
Generate($1:r+".ttf");<br />
Quit(0); </code></p>
<p>Salvar o script com o nome de <em>otf2ttf.sh</em> e então executar ele com o comando:</p>
<p><code>fontforge -script otf2ttf.sh FONTNAME.otf </code></p>
<p>Caso se tenha que converter muitas fontes, que foi o meu caso, pode-se executar o sript assim:</p>
<p><code>for i in *.otf; do fontforge -script otf2ttf.sh $i; done</code></p>
<p>Pronto, meus problemas foram resolvidos.</p>
<p><strong>EDITADO EM 07/10/2009: <em>Este post só menciona o Linux, mas o Fontforge funciona também no Windows, mas precisa que o <a href="http://www.cygwin.com/">Cygwin</a> esteja instalado.</em></strong></p>
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<title><![CDATA[Easy Introduction to Git]]></title>
<link>http://alecthegeek.wordpress.com/2009/09/04/easy-introudction-to-git/</link>
<pubDate>Fri, 04 Sep 2009 01:29:12 +0000</pubDate>
<dc:creator>Alec</dc:creator>
<guid>http://alecthegeek.wordpress.com/2009/09/04/easy-introudction-to-git/</guid>
<description><![CDATA[I&#8217;ve just had an article published by Sitepoint that aims to introduce Git to people who may n]]></description>
<content:encoded><![CDATA[I&#8217;ve just had an article published by Sitepoint that aims to introduce Git to people who may n]]></content:encoded>
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<title><![CDATA[Metasploit + Cygwin + autopwn (in Windows Vista)]]></title>
<link>http://brainsturm.wordpress.com/2009/08/27/metasploit-cygwin-autopwn-in-windows-vista/</link>
<pubDate>Thu, 27 Aug 2009 11:51:49 +0000</pubDate>
<dc:creator>brainsturm</dc:creator>
<guid>http://brainsturm.wordpress.com/2009/08/27/metasploit-cygwin-autopwn-in-windows-vista/</guid>
<description><![CDATA[Ich hatte neulich eine Idee. Es sollte doch möglich sein Metasploit und autopwn unter Vista laufen z]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Ich hatte neulich eine Idee.<br />
Es sollte doch möglich sein Metasploit und autopwn unter Vista laufen zu lassen. Mein Notebook ist ja grad defekt und ich will kein Dual-Boot (Vista &#38; Ubuntu o.ä.) auf das Leihgerät packen&#8230;..der Aufwand ist mir zu hoch, für die Zeit, in der ich das Gerät noch nutze. Also muss es doch mit Cygwin funktionieren. Es ist mir gelungen und ich habe das sogar aufgezeichnet!</p>
<p>Ich habe ein kleines Step-By-Step HowTO  geschmiedet. Bitte gebt mir einen Kommentar, ob es funktioniert oder ob etwas fehlt:<!--more--></p>
<p>1. cygwin downloaden (<a href="http://cygwin.com/setup.exe" target="_blank">http://cygwin.com/setup.exe</a>)<br />
2. setup.exe ausführen<br />
3. Wizard bis zum &#8220;Select Packages&#8221;<br />
4. Folgende Packete sind zu installieren</p>
<blockquote><p>- wget<br />
- tar<br />
- ruby<br />
- readline<br />
- Subversion<br />
- nano/vim<br />
- gcc g++ compiler<br />
- make<br />
- sqlite3<br />
- libsqlit3-devel</p></blockquote>
<p>4. Kompatibilitätsmodus ändern</p>
<blockquote>
<p style="text-align:left;">a) Rechts-Klick auf &#8220;C:\Cygwin\bin\wget.exe&#8221;<br />
b) &#8220;Eigenschaften&#8221; klicken<br />
c) Reiter &#8220;Kompatibilität&#8221; -&#62; &#8220;Programm im Kompatibilitätsmodus ausführen für:&#8221; &#8211;&#62; &#8221;Windows XP (Service Pack 2)&#8221; auswählen<br />
&#8212;&#8211; Die selbe Prozedur für folgende durchführen &#8212;&#8211;<br />
+ die &#8220;Cygwin&#8221;-Verknüpfung auf dem Desktop und Startmenü</p></blockquote>
<p>5. Cygwin wieder starten<br />
6. NOW I will use the sqlite-db-server</p>
<blockquote><p>- &#8220;wget <a href="http://sqlite.org/sqlite-3.6.17.tar.gz" target="_blank">http://sqlite.org/sqlite-3.6.17.tar.gz</a>&#8220;<br />
- &#8220;tar xvf sqlite-3.6.17.tar.gz&#8221;<br />
- &#8220;cd sqlite-3.6.17&#8243;<br />
- &#8220;./configure&#8221;<br />
- &#8220;make&#8221; // ignore the warnings<br />
- &#8220;make install&#8221; // ignore the warnings</p>
<p>If you got an memory-error-message and &#8216;make&#8217;, like:<br />
<img class="size-full wp-image-186 alignleft" title="erroro_cygwin" src="http://brainsturm.wordpress.com/files/2009/08/erroro_cygwin.jpg" alt="erroro_cygwin" width="510" height="14" /></p>
<pre style="margin:0;"><tt>7<tt> [main] ? (232756) C:\cygwin\bin\sh.exe: *** fatal </tt><tt>error - could </tt><tt>n't allocate heap, Win32 error 487, base </tt>
0x6D0000, top 0x6E0000, </tt><tt>reserve_size 61</tt>
440, allocsize 65536, page_const 4096</pre>
</blockquote>
<p>Take a look at <a href="http://cygwin.com/faq/faq.using.html#faq.using.bloda" target="_blank">http://cygwin.com/faq/faq.using.html#faq.using.bloda</a> for the solution.</p>
<p>7. Download and install RubyGem</p>
<blockquote>
<p style="text-align:left;">- &#8220;wget <a href="http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz" target="_blank">http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz</a>&#8220;<br />
- &#8220;tar xvf rubygems-1.3.5.tgz&#8221;<br />
- &#8220;cd rubygems-1.3.5&#8243;<br />
- &#8220;ruby setup.rb install&#8221; # this process needs some time #</p></blockquote>
<p>8. Update RubyGems by running the following:</p>
<blockquote><p>- &#8220;gem update &#8211;system&#8221;</p></blockquote>
<p>9. Install ActiveRecord and sqlite3-ruby</p>
<blockquote><p>- &#8220;gem install activerecord&#8221; // needs some time</p></blockquote>
<p>10. Download the Framework</p>
<blockquote><p>- go to &#8220;<a href="http://www.metasploit.com/" target="_blank">http://www.metasploit.com/</a>&#8220;<br />
- wget the actuall framework<br />
- &#8220;tar xvf framework-3.2.tar.bz2&#8243; // used th 3.2 for this tutorial</p></blockquote>
<p>11. Update the framework</p>
<blockquote><p>- &#8220;cd framework-3.2&#8243;<br />
- &#8220;svn co http://metasploit.com/svn/framework3/trunk/ *&#8221;<br />
- &#8220;svn update&#8221;</p></blockquote>
<p>12. Instal the db-driver</p>
<blockquote><p>- Enter &#8220;gem install sqlite3-ruby&#8221;</p></blockquote>
<p>13. Run the autopwn</p>
<blockquote><p>- &#8220;cd framework-3.2&#8243;<br />
- &#8220;./msfconsole&#8221;<br />
- &#8220;load db_sqlite3&#8243;<br />
OUTPUT:<br />
[*] Successfully loaded plugin: db_sqlite3</p>
<p>- &#8220;db_create&#8221;<br />
OUTPUT:<br />
[*] The specified database already exists, connecting<br />
[*] Successfully connected to the database<br />
[*] File: C:\Users\&#60;YOU&#62;\AppData\Local/.msf3/sqlite3.db</p>
<p>- run &#8220;db_autopwn&#8221;</p></blockquote>
<p>13.1 If you want to run &#8220;db_nmap&#8221;, it will give an error-message like &#8220;<br />
[*] exec: &#8220;/usr/bin/nmap&#8221; &#8220;-PN&#8221; &#8220;192.168.1.2&#8243; &#8220;-oX&#8221; &#8220;/cygdrive/c/Users/DR8BD7~1.FLA/AppData/Local/Temp/dbnmap20090827-4896-uon6bs-0&#8243;.</p>
<p>But first you have to get the &#8220;nmap.exe&#8221; (don&#8217;t forget to change the &#8220;Compatibility mode&#8221; like step 4) and put this file into &#8220;C:\cygwin\bin&#8221;.</p>
<p>Against that you have to do the following:</p>
<blockquote>
<p style="text-align:left;">1. Create a file without content like<br />
&#8220;C:\cygwin\home\&#60;YOU&#62;\framework-4.2\dbnmap.xml&#8221;<br />
2. Open up<br />
&#8220;C:\cygwin\home\&#60;YOU&#62;\framework-3.2\lib\msf\ui\console\command_dispatcher\db.rb\ with your favorite text-editor<br />
3. Change line 484 or so</p>
<pre style="text-align:left;">     fd = Tempfile.new('dbnmap')
     INTO
     fd = File.open('C:/cygwin/home/Dr.Flash/framework-3.2/dbnmap.xml', "r+")</pre>
<p style="text-align:left;">4. Try &#8220;db_nmap &#60;IP-Adress&#62;&#8221; again and it should work</p>
</blockquote>
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<title><![CDATA[Review on NMR software]]></title>
<link>http://sciart.wordpress.com/2009/08/23/review-on-nmr-software/</link>
<pubDate>Sun, 23 Aug 2009 22:24:49 +0000</pubDate>
<dc:creator>jokertsai</dc:creator>
<guid>http://sciart.wordpress.com/2009/08/23/review-on-nmr-software/</guid>
<description><![CDATA[As a modern technique developed since 1950s, Nuclear Magnetic Resonance (NMR) has been a routine wor]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>As a modern technique developed since 1950s, Nuclear Magnetic Resonance (NMR) has been a routine work for Chemists and Structural biologists. However, as the technique still evolving, no gold standards have been set for software tools, which poses a sticky situation for newcomers.</p>
<p>Here I am reviewing some NMR software based on my own experience.</p>
<p>Category I: NMR Processing software</p>
<p>1. Xwin-NMR/TopSpin</p>
<p>The default NMR Processing software that comes with Bruker NMR Spectrometer. I have been using both on 500 MHz and 800 MHz Bruker NMR spectrometer respectively and they are still my top priorities with regard to data processing. The only shortcoming I could think of is that XwinNMR could not be used to process the data collected with TopSpin, which is the successor of the former one. Other than that, Xwin-NMR/TopSpin provide a convenient way for processing, including baseline correction with different modes, and substraction of 1D slice from 2D spectrum. Another plus is the appendant software Xwinplot, which makes good plots such as overlay of two spectra.</p>
<p>My recent experience with 15N relaxation rate analysis exposed another problem of XwinNMR. You need to be very careful about the intensities of the peaks in a series of spectra. Depending on the display settings of XwinNMR, you may have two fold stronger or weaker resonances when the spectra are rendered by NMRViewJ at the same plot level. Thus, your T1 or T2 data may not fit on an exponential curve.</p>
<p>2. <a title="NMRPipe" href="http://spin.niddk.nih.gov/NMRPipe/">NMRPipe</a></p>
<p>A free NMR processing software which can be installed on Windows XP with SFU 3.5. I have used this free software for a while but finally dropped it. It doesn&#8217;t support the plotting function as Xwinplot does. Moreover, the processing is not so intuitive as XwinNMR.</p>
<p>3. <a title="MestRe Nova Lite" href="http://www.mestrec.com/index.php?idp=4&#38;i18n=1">MestRec</a></p>
<p>Another free software that could be operated on Windows XP. It seems has been upgraded to MestRe Nova Lite. It is simple to use however also for simple processing (i.e. 1D processing) only. You may consider the formal version, but I have never tried.</p>
<p>4.<a href="http://www.inmr.net/index.html#SiteMap"> iNMR</a></p>
<p>I have heard quite a lot of compliments about this one, but was not able to try out myself. You have to be a Mac user to use iNMR. Also, there is no free lunch. The standard license fee is about 500 euros.</p>
<p>Category II: Spectrum visualization and analysis</p>
<p><a href="http://www.onemoonscientific.com/nmrview/summary.html">NMRViewJ</a></p>
<p>This is the only software that I use for visualizing spectrum, peak picking and chemical shift assignment, automatic relaxation rate analysis. It is free, and easy to handle on Windows XP. The only disadvantage is that you need to bring up too many windows for doing your work. It seems that there is no way to put an logical order for the layers of windows. Meanwhile, I am hoping to see a better manual, although the current one does not hurt the program to be good.</p>
<p>Category III: Automated assignment and structural calculation</p>
<p>1. <a title="CYANA" href="http://www.las.jp/english/products/s08_cyana/index.html">CYANA 2.1</a>/DYANA</p>
<p>CYANA (Combined  Assignment and dynamics Algorithm for NMR application) is the software that I use for protein Structural calculation. I basically chose it for several reasons: The software enables an automated NOE assignment as long as you have your chemical shift assignments ready. The peak lists generated from NMRView can be imported directly to CYANA. The new CYANA is also able to convert the distance restraints from the CYANA version to XPLOR/CNS version. You can run the program on Linux or a Windows XP system loaded with Cygwin. (By the way, I can not say enough good words about <a title="Cygwin" href="http://www.cygwin.com/">Cygwin</a>.)</p>
<p>What I don&#8217;t like about CYANA is that the program has an out-of-date manual which originally was for DYANA 1.5, while the program has progressed to CYANA 2.1. This is not what I would expect from a program that costs $600 euros. The company, L.A.Systems Inc in Japan, who takes charges of the selling never get back efficiently about questions other than purchasing. What I am glad is that the author of CYANA, Dr. Peter  Güntert is working on a <a href="http://www.cyana.org/wiki/index.php/Main_Page">CYANA Wiki</a> with his team. I am really looking forward to seeing more tutorials on the CYANA and also a release of 3.0 version.</p>
<p>2. <a title="XPLOR-NIH" href="http://nmr.cit.nih.gov/xplor-nih/">XPLOR-NIH</a></p>
<p>A free soft ware based on XPLOR for structure determination by using X-Ray Crystallography or NMR. However, I have never used it for structure calculation. What I am working on right now is to use this program for energy minimization.</p>
<p>Unlike the CYANA, XPLOR-NIH requires an Linux system for installation. It will also take you some time to figure out the ways to generate required files in correct format.</p>
<p>3. <a title="CNS" href="http://cns-online.org/v1.21/">CNSsolve</a></p>
<p>Another free software developed on XPLOR. I personally don&#8217;t use CNSsolve as it does not provide automated NOE assignment.</p>
<p>Category IV: Structure Analysis</p>
<p>1. <a title="Procheck-NMR" href="http://www.biochem.ucl.ac.uk/~roman/procheck_nmr/procheck_nmr.html">Procheck-NMR</a></p>
<p>After the structure is calculated, you need a way to do &#8220;quality control&#8221;. So here comes Procheck-NMR. I recently figured out to install it on Windows XP with Cygwin. What you need to do is to change the .bashrc file accordingly.</p>
<p>2. <a title="MolMol" href="ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/">MolMol</a></p>
<p>An easy-to-use software enables you to Fit different structures and calculate RMSDs. It also provides tools to display three dimensional structures in different views. Works perfectly on Windows XP.</p>
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<title><![CDATA[text browsing in cygwin]]></title>
<link>http://kasolutions.wordpress.com/2009/08/19/text-browsing-in-cygwin/</link>
<pubDate>Wed, 19 Aug 2009 11:35:32 +0000</pubDate>
<dc:creator>aneeska</dc:creator>
<guid>http://kasolutions.wordpress.com/2009/08/19/text-browsing-in-cygwin/</guid>
<description><![CDATA[why in the world would someone want to do text browsing? when the browser war is reaching its pinnac]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>why in the world would someone want to do text browsing? when the browser war is reaching its pinnacle with all the major players vying to eat out on IE&#8217;s market share, here is a guy talking about text-browsing! is he nuts?</p>
<p>well not exactly! we at home are sharing a broadband connection. People out there torrent a lot. That means there is little bandwidth left to browse for others. Thats when I began to appreciate text browsing.</p>
<p>The application is called &#8220;<strong>links</strong>&#8221; which could be used in cygwin. Download the package from <a href="http://ftp.daum.net/cygwin/release/links/" target="_blank">here</a>.</p>
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<title><![CDATA[Cygwin - O Linux no Windows]]></title>
<link>http://marcosvidolin.wordpress.com/2009/08/15/cygwin-o-linux-no-windows/</link>
<pubDate>Sat, 15 Aug 2009 20:00:31 +0000</pubDate>
<dc:creator>marcosvidolin</dc:creator>
<guid>http://marcosvidolin.wordpress.com/2009/08/15/cygwin-o-linux-no-windows/</guid>
<description><![CDATA[Olá pessoal, segue mais um post aqui no blog, agora mostrando um pouquinho do poderoso Cygwin. O Cyg]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><div class="mceTemp mceIEcenter" style="text-align:left;">Olá pessoal, segue mais um post aqui no blog, agora mostrando um pouquinho do poderoso Cygwin.</div>
<p>O Cygwin é um programa que pode ser instalado no Windows a fim de trazer um pouco do poder do Linux para o sistema da Microsoft de forma simples e pratica, sem a necessidade de particionar o HD, fazer dual-boot ou ter que reiniciar o computador quando quiser usar um ou outro sistema. Ele se torna um programa do Windows, uma janela rodando o Linux.</p>
<p>O Cygwin é uma ótima opção para quem estiver pensando em migrar gradativamente para o Linux e não quer abrir mão de uma porção de softwares em que já esta acostumado a usar, ou até mesmo para aqueles que usam o Windows no ambiente de trabalho e quer tirar proveito da consola do Linux (como no meu caso&#8230; :b ).<br />
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Ok chega de papo e vamos aos passos para a instalação:</p>
<p>1- Baixe o executável da aplicação no seguinte link: <a href="http://www.cygwin.com/setup.exe">http://www.cygwin.com/setup.exe</a><br />
2- Execute o arquivo setup.exe<br />
3- Será apresentado a tela de Release. Clique no famoso “Avançar &#62;”.<br />
4- Em seguida deixe a opção trazida por default “Install from Internet” e clique em “Avançar &#62;”.<br />
5- Nesta tela mantenha o diretório “c:\cygwin“ como (Root Directory) e as outras opções marcadas como a imagem abaixo.</p>
<p><img class="aligncenter size-full wp-image-14" title="Root Directory" src="http://marcosvidolin.wordpress.com/files/2009/08/img12.jpg" alt="Root Directory" width="450" height="349" /> </p>
<p>6- Escolha o diretório onde os pacotes de instalação serão baixados.</p>
<p><img class="aligncenter size-full wp-image-15" title="Local Package" src="http://marcosvidolin.wordpress.com/files/2009/08/img2.jpg" alt="Local Package" width="450" height="349" /></p>
<p>7- Selecione o tipo de conexão que você prefere/possui e avance.</p>
<p><img class="aligncenter size-full wp-image-16" title="Connection Type" src="http://marcosvidolin.wordpress.com/files/2009/08/img3.jpg" alt="Connection Type" width="450" height="349" /></p>
<p>8- Escolha um dos sites de downloads apresentados e avance.<br />
9- Em seguida mantenha os pacotes trazidos por default e clique em “Avançar &#62;”. Caso deseje adicionar outros pacotes no seu Cygwin, após concluir a instalação execute novamente o setup.exe e selecione os pacotes extras desejados.</p>
<p><img class="aligncenter size-full wp-image-17" title="Packages" src="http://marcosvidolin.wordpress.com/files/2009/08/img4.jpg" alt="Packages" width="450" height="349" /></p>
<p>Prontinho! Assim que terminar o download dos pacotes o processo de instalação ira iniciar e você poderá usá-lo assim que terminar, sem ao menos reiniciar o computador.</p>
<p>Pratico não!?! Agora você já pode utilizar um cat, grep, etc&#8230; Ah, tem mais! Também é possível adicionar alguns pacotes extras de gerenciadores gráficos como o KDE, Gnome entre outros.</p>
<p><img class="aligncenter size-full wp-image-18" title="Terminal" src="http://marcosvidolin.wordpress.com/files/2009/08/img5.jpg" alt="Terminal" width="450" height="211" /></p>
<p><img class="aligncenter size-medium wp-image-19" title="Desktop" src="http://marcosvidolin.wordpress.com/files/2009/08/img6.jpg?w=300" alt="Desktop" width="300" height="188" /></p>
<p>Referencias:</p>
<p><a href="http://www.cygwin.com/">http://www.cygwin.com/</a><br />
<a href="http://aurelio.net/cygwin/#toc1">http://aurelio.net/cygwin/#toc1</a></p>
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<title><![CDATA[Erlang-mode with Emacs on Cygwin]]></title>
<link>http://ntdt.wordpress.com/2009/07/27/erlang-mode-with-emacs-on-cygwin/</link>
<pubDate>Mon, 27 Jul 2009 08:41:00 +0000</pubDate>
<dc:creator>ntdt</dc:creator>
<guid>http://ntdt.wordpress.com/2009/07/27/erlang-mode-with-emacs-on-cygwin/</guid>
<description><![CDATA[Run setup.exe of Cygwin then select the package emacs. Once the install of emacs done, edit your $HO]]></description>
<content:encoded><![CDATA[<div class='snap_preview'><p>Run setup.exe of Cygwin then select the package emacs. Once the install of emacs done, edit your $HOME/.emacs with the following content</p>
<blockquote><p>(setq load-path (cons &#8220;/cygdrive/c/erl/lib/tools-2.6.4/emacs&#8221; load-path))<br />
(setq erlang-root-dir &#8220;/cygdrive/c/erl&#8221;)<br />
(setq exec-path (cons &#8220;/cygdrive/c/erl/bin/&#8221; exec-path))<br />
(require &#8216;erlang-start)
</p></blockquote>
<p>where Erlang is installed under c:/erl</p>
<p>Now load your emacs with an erlang source code file.</p>
<p>For references:</p>
<ul>
<li><a href="http://erlang.org/doc/man/erlang_mode.html">http://erlang.org/doc/man/erlang_mode.html</a></li>
<li><a href="http://bc.tech.coop/blog/070528.html">http://bc.tech.coop/blog/070528.html</a></li>
</ul>
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