Installing Pysam for windows

[Mark2]

Hello.

I need a way to work with BAM files and as I am somewhat familiar with Python (2.7) I wanted to use the module pysam. However, it has proven rather troublesome to install on my pc (Windows 8, 64 bit).

When I first tried to install it, I got an error about not having Microsof Visual C++; I subsequently downloaded visual c++ compiler. Now when I try to install it (no matter how, whether with pip, easy_install, or whatever) I still get an error:

cl : Command line error D8021 : invalid numeric argument '/Wno-error=declaration
-after-statement'

error: command 'C:\\Users\\Mark\\AppData\\Local\\Programs\\Common\\Microsoft\\Vi
sual C++ for Python\\9.0\\VC\\Bin\\cl.exe' failed with exit status 2

I've tried several suggestions from stackoverflow; insalling 32-bit python instead of 64 (which supposedly caused some problems for others); I tried using an older version of pip when I thought pip might not be working (there was an issue with newer versions having some SSN issue when trying to install packages). Still no solution.

So if anyone can give me a detailed explanation for how to effectively install pysam I would much appreciate it.

Alternatively, if there's an easier way to work with BAM files, any suggestions are welcome. I recently installed cygwin on my pc for other purposes but perhaps I could use SAMtools via cygwin. Any suggestions appreciated though, thanks.

[GenoMax]

Are you familiar with command line/unix? If not you can easily pick up the basics by following this guide: http://korflab.ucdavis.edu/Unix_and_Perl/current.html

You can then get around all these issues by using a virtual machine running linux on your PC.

[Mark2]

Are you familiar with command line/unix? If not you can easily pick up the basics by following this guide: http://korflab.ucdavis.edu/Unix_and_Perl/current.html

You can then get around all these issues by using a virtual machine running linux on your PC.

Only a little. I've used the Cygwin unix-like environment a bit. Would using a virtual machine require me to partition my hard drive?

And are you saying this would make it easier to install pysam, or that I could just employ SAMtools from the unix command line?

Thanks.

[GenoMax]

Only a little. I've used the Cygwin unix-like environment a bit. Would using a virtual machine require me to partition my hard drive?

No it would not require partitioning. You would be able to run something like Virtualbox https://www.virtualbox.org/wiki/Downloads and a linux distribution (look into Debian or Ubuntu).

And are you saying this would make it easier to install pysam, or that I could just employ SAMtools from the unix command line?
Thanks.

If your only interest in using pysam is to use samtools-like functionality then it would be simpler to use Samtools natively on unix.

Even though many programs can be made to work in cygwin there will eventually be something that won't work. If you are planning to do significant NGS analysis then consider putting in a week or two to acquire enough unix command line skills.

[Mark2]

No it would not require partitioning. You would be able to run something like Virtualbox https://www.virtualbox.org/wiki/Downloads and a linux distribution (look into Debian or Ubuntu).

If your only interest in using pysam is to use samtools-like functionality then it would be simpler to use Samtools natively on unix.

Even though many programs can be made to work in cygwin there will eventually be something that won't work. If you are planning to do significant NGS analysis then consider putting in a week or two to acquire enough unix command line skills.

Ok, I'm now installing virtual box. Thanks for the suggestion.