This is the view from my desk: perfect, isn't it? Getting back to work :)
Back to the topic, since I'm using a laptop installed with Windows 8.1, I was thinking of running PLINK on the laptop, provided I have enough HDD space and RAM, of course. I think with 6GB of RAM, I should be able to do quite a bit before I crash it. A tiny search on PLINK website led me to the MS-DOS version of PLINK, which means I could do the genomic analysis offline without using my group's server! Another yay!
Here's the instruction as per PLINK website on how to download and install PLINK on Windows... I think the links on my page would lead you to the download site, further instructions and manuals for PLINK. Enjoy using the whole genome association analysis toolset!
This page contains some important information regarding how to set up and use PLINK. Individuals familiar with using command line programs can probably skip most of this page. DownloadPLINK is now available for free download. Below are links to ZIP files containing binaries compilied on various platforms as well as the C/C++ source code. Linux/Unix users should download the source code and compile (see notes below). These downloads also contain a version of gPLINK, an (optional) GUI for PLINK. Please see these pages for instructions on use of gPLINK. Remember This release is considered a stable release, although please remember that we cannot guarantee that it, just like most computer programs, does not contain bugs...
One more thing... If you download PLINK please either join the very low-volume e-mail list (link from Introduction page) or drop an e-mail to plink AT chgr dot mgh dot harvard dot edu letting me know you've downloaded a copy. For old versions of PLINK please visit the archive. Debian users PLINK is available as a Debian package, see these notes. Note, the executable is named snplink in the Debian plink package. Development version source codeYou can download the very latest development source code in this ZIP file. This is really, strongly not recommended for most users. The code posted here could change on a daily basis and is not versioned. Development source code versions have a p suffix, meaning pre-release. For example, if the current release is 1.04, the next stable release will be 1.05 and the development code will be 1.05p. Note that 1.05 may differ from 1.05p and as noted before, from day-to-day the 1.05 development code may change in any case. The principle reason for including the source code here is to allow access for specific users to specific, new features. These features are described here. General installation notesThe PLINK executable file should be placed in either the current working directory or somewhere in the command path. This means that typing plinkor ./plinkat the command line prompt will run PLINK, no matter which current directory you happen to be in. PLINK is a command line program -- clicking on an icon with the mouse will get you nowhere. Below, on this page, is a general overview of how to use the command line to run PLINK. The next sections give details about how to install PLINK on different platforms. Windows/MS-DOS notesUnzipping the downloaded ZIP file should reveal a single executable program plink.exe. The Windows/MS-DOS version of PLINK is also a command line program, and is run by typing plink {options...}not by clicking on the icon with the mouse. Open a DOS windows by selecting "Command Prompt" from the start menu, or entering "command" or "cmd" in the "Run..." option of the start menu. The folders c:\windows\ or c:\winnt\ are typically in the path, so these are good places to copy the file plink.exe to. You can copy the plink.exe file using Windows, as you would copy-and-paste any file (e.g. using the right-button menu or the keyboard shortcuts control-C (paste) and control-V (paste). Alternatively, if you know that you will only ever run PLINK on files in a single folder, then you can paste plink.exe into that folder, e.g. C:\work\genetics\. The disadvantage of this approach is that PLINK will not be available from the command line if you are in a folder other than this one. Once you have copied plink.exe to the correct location, you can test whether or not PLINK is available (i.e. in your command path) by simply typing plinkat the command line. You should see something like the following message: Microsoft Windows XP [Version 5.1.2600]
(C) Copyright 1985-2001 Microsoft Corp.
C:\>plink
@----------------------------------------------------------@
| PLINK! | v0.99l | 27/Jul/2006 |
|----------------------------------------------------------|
| (C) 2006 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@
Web-based version check ( --noweb to skip )
Connecting to web... OK, v0.99l is current
*** Pre-Release Testing Version ***
Writing this text to log file [ plink.log ]
Analysis started: Fri Jul 28 10:07:57 2006
Options in effect:
ERROR: No file [ plink.ped ] exists.
Do not worry about this error message -- normally you would specify your own PED/MAP file names to analyse (i.e. the default input filename is plink.ped). Please ask your system administrator for help if you do not understand this. HINT In MS-DOS, you can to increase the width of the window to avoid output lines wrapping around and being hard to read. To do this under Windows XP DOS: right click on the top title/menu bar of the window and select Properties / Layout / Window Size / Width -- increse the width value to a larger value (e.g. 120, or as large as possible without the window getting too big to fit on your screen!). |
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Positive suggestions help to keep me going. Thanks! :)