====== Mac Basic Setup ======

===== Applications =====
==== Basic ====
  * [[http://www.mozilla.com/firefox/|Firefox]]: web browser
  * [[http://www.barebones.com/products/TextWrangler/|TextWrangler]]: text editor
  * [[http://filezilla-project.org/|FileZilla]]: ''sftp'' client
  * [[http://download.openoffice.org/|OpenOffice]]
  * MS Office available from the IPMB IT office (AS site license)

==== Optional ====
  * gcc: C compiler, install using the Xcode Tools (under ''Download Software/Developer Tools'' on the [[http://developer.apple.com/|Apple Developer Connection]]).

  * [[http://perltidy.sourceforge.net/|Perltidy]]: utility to tidy up perl codes
  * [[http://www.gnu.org/software/wget//|Wget]]: command-line utility to fetch files 

  * [[http://www.gelanalyzer.com/|GelAnalyzer]]: electrophoresis gel image analyzer (Java-based)
  * [[http://www.jalview.org/|Jalview]]: multiple sequence alignment viewer (Java-based)
  * [[http://tree.bio.ed.ac.uk/software/figtree/}FigTree]]: phylogenetic tree viewer

  * [[http://www.r-project.org/|R]]: software environment for statistical computing and graphics

  * [[http://www.macports.org/|MacPorts]]
  * [[http://www.finkproject.org/|Fink]]

  * [[http://www.videolan.org/vlc/download-macosx.html|VLC]]: media player.

===== System Preferences =====
  * Energy Saver: Computer sleep = **never**, Display sleep = **10 min**, shutdown when UPS battery level is **below 20%**, **enable** start up automatically after a power failure.
  * Print & Fax: add lab printer
  * Network: set up lab intranet using DHCP. If using a desktop with ethernet connect, turn off Wi-Fi
  * Bluetooth: **off** (unless wireless keyboard/mouse is used)
  * Sharing: set **Computer Name**, enable **File Sharing** and **Remote Login**
  * Accounts: disable **Automatic login**, display login window as **Name and password**, enable **Show input menu in login window**


===== Backup =====
  * Assign one external hard drive for each mac workstation as the Time Machine backup drive.

===== Network =====
  * Use Terminal, type ''networksetup -listallnetworkservices'' to see the list of network services 
    * e.g., ''Ethernet'' and ''Wi-Fi''
  * IPv6; often cause problems
    * to disable: ''sudo networksetup -setv6off Ethernet'' and/or ''sudo networksetup -setv6off Wi-Fi''
    * to enable: ''sudo networksetup -setv6automatic Ethernet'' and/or ''sudo networksetup -setv6automatic Wi-Fi''

===== xcode =====
<code>
# Mac OS X 10.9.4
xcode-select --install
</code>

===== Extended Attributes =====
Some files may have extended attributes, for example:
<code bash>
chkuo@mesquite[~]$ ls -l
-rwxr-xr-x@   1 chkuo  staff   3454 Jan 22 11:11 file1*
-rwxr-xr-x    1 chkuo  staff   2628 Nov  2  2006 file2*
</code>

The ''@'' symbol after the permission info of ''file1'' indicates that there are extended attributes. To find out more details:
<code bash>
chkuo@mesquite[~]$ ls -@l *
-rwxr-xr-x@   1 chkuo  staff   3454 Jan 22 11:11 file1*
	com.apple.FinderInfo	  32 
	com.apple.TextEncoding	  15 
-rwxr-xr-x    1 chkuo  staff   2628 Nov  2  2006 file2*
</code>

To get rid of these extended attributes:
<code bash>
chkuo@mesquite[~]$ xattr -d com.apple.FinderInfo file1
chkuo@mesquite[~]$ xattr -d com.apple.TextEncoding file1
</code>


===== Newline characters =====
Mac OS X and Unix uses different characters to denote newline break. This can cause problem when you need to manipulate files in Finder and Terminal. To convert between the two, use:

<code bash>
#!/bin/sh
# change linefeed from unix to mac
for x
do 
  echo "$x"
  tr '\012' '\015' < "$x" > "tmp.$x"
  mv "tmp.$x" "$x"
done
</code>

Or:
<code bash>
#!/bin/sh
# change linefeed from mac to unix
for x
do 
  echo "$x"
  tr '\015' '\012' < "$x" > "tmp.$x"
  mv "tmp.$x" "$x"
done
</code>

===== Job scheduling =====
In addition to the use of ''crontab'' for reoccurring jobs, you can also use the ''at'' utility to schedule a job to run at a pre-determined time. By default, this utility is disabled due to power management issue (need to read hard drive every minute). This is more of a problem for laptops, but not so for servers (or desktops that are being used as servers). To turn it on, use the command:
<code bash>
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.atrun.plist
</code>

To turn it off again, use:
<code bash>
sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.atrun.plist
</code>

To check if the ''at'' utility is disabled or not, check preference file to see if ''Disabled'' is specified:
<code bash>
cat /System/Library/LaunchDaemons/com.apple.atrun.plist
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>Label</key>
    <string>com.apple.atrun</string>
    <key>ProgramArguments</key>
    <array>
	    <string>/usr/libexec/atrun</string>
    </array>
    <key>StartInterval</key>
    <integer>30</integer>
    <key>Disabled</key>
    <true/>
</dict>
</plist>
</code>

For more details, read [[http://www.macosxhints.com/article.php?story=20050921214411382]]


===== Maintenance =====
==== Check Time Stamps ====
Check when the maintenance scripts were run:
<code bash>
ls -al /var/log/*.out
</code>

Output should look like this:
<code bash>
chkuo@mesquite[~]$ ls -al /var/log/*.out
-rw-r--r--  1 root  wheel  91407 Jun 18 10:39 /var/log/daily.out
-rw-r--r--  1 root  wheel     84 Jun 18 10:58 /var/log/monthly.out
-rw-r--r--  1 root  wheel   3625 Jun 18 10:57 /var/log/weekly.out
</code>

==== Manual Execution ====
In case the computer was shut down when the scripts were scheduled to run.

<code bash>
sudo periodic daily
sudo periodic weekly
sudo periodic monthly
</code>

Or, to run all three at once:
<code bash>
sudo periodic daily weekly monthly
</code>

==== More Info ====
  * [[http://www.thexlab.com/faqs/maintscripts.html|http://www.thexlab.com/faqs/maintscripts.html]]
  * [[http://managingosx.wordpress.com/2008/06/18/launchd-vs-periodic/|http://managingosx.wordpress.com/2008/06/18/launchd-vs-periodic/]]





===== Troubleshooting =====
  * [[http://support.apple.com/kb/HT3964|Resetting the System Management Controller (SMC)]]
  * [[http://support.apple.com/kb/HT1379|Resetting the PRAM and NVRAM]]