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Old 06-04-2010, 12:07 PM   #1
Location: Alabama

Join Date: Jun 2010
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Default samtools on windows?


I'm new to next-gen sequence analysis and am trying to analyze data from my first project. I have been provided .sam files to look at my data, with instruction to look at it in samtools. However, when I download samtools, and attempt to open the program, the program opens for a split second, then immediately closes with no error messages. Is samtools compatible with Windows XP or is there another program that I'm going to need to use?

Thanks for any insight,
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Old 06-04-2010, 04:54 PM   #2
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Install this:

And then download and install samtools from within cygwin.

Cygwin installs a dll that provides an linux API emulation layer.
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Old 06-08-2010, 07:39 AM   #3
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Sorry, I got the same problem. I have downloaded Samtools from sourceforge for the windows version. I question is where to put all these files? I could put .exe in my perl\bin directory. What about others?

I tried to compile it using MSYS and it has many dependencies...

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Old 08-05-2010, 05:14 AM   #4
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Which commands do you use from within cygwin to install samtools?
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