Blast+ On Windows

Question

[Vivek]

I need to compile blast+ on windows.

Can someone tell me how do i do this.I tried Visual studio 2010,but i get an error saying that some project tree builder is not found.

I am a beginner so please be a little detailed with your answer.

Thanks

[Michael]

Forget Visual Studio. You can download a binary, why would you want to compile it on windows? It looks like blast+ on window is best built under Cygwin (http://www.cygwin.com/), there is a build script in the c++/compilers/cygwin folder. This is not a beginner task though, and porting to a different compiler suite is definitely something I would abstain from.

Answer 1

[Obi Griffith]

If you have tasks requiring blast+ that go beyond the capabilities of the blast web interface then I second Michael's comment of just downloading a binary. NCBI provides detailed instructions of how to run blast+ on a windows machine without trying to compile yourself.

However, I also suggest that you consider moving into a *nix environment. If you have only a windows machine available you can install VMware and then put a linux distro like Ubuntu on it. Or, you can try DNALinux, a preconfigured virtual machine with applications targeted for bioinformatics (including blast) that runs on top of the VMWare Player. You'd have to bite the bullet and learn some basic linux to get you started. But, in the long run, if you're doing bioinformatics this is the way to go (IMHO).

[Hamish]

Agreed. Using a virtual machine (VM) can make things much easier, especially when coupled with a Linux distribution with the appropriate tools (see http://en.wikipedia.org/wiki/BioLinux for some additional options). I have to say that I prefer VirtualBox (https://www.virtualbox.org/) over VMware for VM on the desktop.

[Daniel]

+1 for biolinux

Answer 2

[Hamish]

As Michael and Obi have said if you just need the NCBI BLAST+ binaries for MS Windows, you can get them from the NCBI, see "Download BLAST Software and Databases" for details.

If you really need to build NCBI BLAST+ from source, you'll have to use the NCBI C++ Toolkit. The NCBI C++ Toolkit contains various applications and programing libraries and includes the NCBI BLAST+ programs. For details of how to build on MS Windows, using MS Visual C++ (included in MS Visual Studio) or Cygwin, see the "MS Windows" section of chapter 4 ("4. Configure, Build, and Use the Toolkit") in "The NCBI C++ Toolkit Book".

If you have problems with the documented procedure, see "30. FAQs, Useful Documentation Links, and Mailing Lists" for details of some common problems and a set of mailing lists can be used to get help with the NCBI C++ Toolkit.

[Michael]

compiling blast using visual studio might be a bit easier than I had thought. Still, I think one needs to know the compilers already quite well to do this right.

[Hamish]

I agree. The process does not look to be for the faint of heart. In my opinion it is better to avoid this if possible and use the provided binaries. While I have built BLAST from source on UNIX a time or several, I was never completely happy with doing it.