Transcript Introduction to Genetics and Genomics

Perl
• Note, I am hoping that we can
accomplish all we need to with CSS
accounts, Linux, and the NoMachine
client -- since these already have Perl
installed.
• However, if you are feeling adventurous,
or want to run Perl locally (on your own
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machine)…
Easiest way to install Perl
• Note, perl typically comes on a Mac or Linux - so if you use these -- you should first check
if it is already installed.
• These instructions are for Windows XP -- (as
of 8/28/2007). They may not work with Vista.
If you try, and they do -- please let me know
• I expect students to spend time with perl
outside of class and "figure this out."
However, if you run stuck, please ask for
help.
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Easiest way to Install Perl
Go to:
http://www.activestate.com/store/activeperl/do
wnload
Click "continue" (registering is optional)
Under "ActivePerl 5.8.8.822" (or close to this)
Select "MSI" under "Windows (x86)"
Save file to Disk (such as the desktop is fine)
Now click on the file what was downloaded
(something like: ActivePerl-5.8.8.822MSWin32-x86-280952)
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ActivePerl
• Follow the instructions from the Install
Wizard.
• Next. I accept. Next. Next. Next.
Install. (it could take several minutes
depending on how fast your computer
is).
• Click "Finish"
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Easiest way to install perl…
Now, go to:
http://www.eclipse.org/downloads
• Download "Eclipse Classic" for Windows (or
Linux for Linux or Mac for Mac) and save to
disk
• Click on the folder that was downloaded
(probably eclipse-SDK-3.3-win32). This may
be eclipse-SDK-3.3-win32.zip -- in which
case you will need to "unzip" it first.
• Click on "eclipse" folder
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Perl -- easy install cont.
• Click on "eclipse" application (this may be
"eclipse.exe" depending on how your
windows box is set up.
• If you get this message:
"This application may depend on the other
compressed files in this folder.
For the application to run properly, it is
recommended that you first extract all files."
Then select: "Extract all"
Follow the instructions of the "Extraction
Wizard" (this may take several minutes)
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Perl Install -- this really is easy
• Click "Finish"
• On my computer -- the last step created
another folder called "eclipse-SDK.3-3win.32" -- but without the "zipper" in the folder
icon.
• Click on "eclipse-SDK.3-3-win.32" (one
without a zipper in the folder)
• Click "eclipse"
• Click "eclipse" (eclipse.exe)
• Click "OK" for "selecting a workspace"
• eclipse should now install and run
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• Click on "Workbench Icon" -- the big arrow
Perl Plugin for Eclipse
• Once you have eclipse running, go to:
• Help-> Software Updates -> Find and
Install…"
• Select "Search for new features to
install"
• Click "Next"
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Perl Plugin
• Click "New remote site"
• For Name -- type in: EPIC
• For URL -- type in:
http://e-p-i-c.sf.net/updates
Click "OK"
Now the "EPIC" box should be "checked"
Click "Finish"
In the "Updates" window, select "EPIC" (a green
check mark will appear)
Click "Next"
Select "I accept the terms in the license
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agreement"
Perl plugin
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Click "Next"
Click "Finish"
Click "Install All"
Click "Yes" (to restart eclipse)
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In eclipse, now select:
Window->Open Perspective->Other
Select "Perl"
Click OK.
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First Perl Program
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File->new->Perl Project
Type in Project Name: Hello
Click "Finish"
Right Click on the "Hello" project and select
New->Perl File
For "File name" enter: Hello.pl
Click "Finish"
Now you can enter a Perl program in the
middle window. Try this:
print "hello world\n";
Then select: Run->Run. Click on "Yes"
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That's it
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