Bowtie on Windows x64

[yokuyuki]

I'm trying to compile bowtie for Windows x64 using MinGW64. I actually have a working binary for bowtie x64, but I can only get it to compile with BOWTIE_PTHREADS=0. When that is enabled, I get "Error: incorrect register '%eax' used with 'q' suffix" and make for bowtie fails. Anyone know any solution around this? I'm using pthreads from http://sourceforge.net/apps/trac/min...ile%20pthreads

[DWW1505]

I have an operational (with threads) bowtie for Win7-x64 which I could make available if you wish. It comes with the usual disclaimer of warranty. I've run it for about a year with no problems. I will have to locate the notes for compiling though.

[yokuyuki]

I have an operational (with threads) bowtie for Win7-x64 which I could make available if you wish. It comes with the usual disclaimer of warranty. I've run it for about a year with no problems. I will have to locate the notes for compiling though.

That'd be great if you could provide me with it. If you have compiling notes to share too, that'd be helpful too for future/similar compilations. You wouldn't happen to have a working version of TopHat too?

[DWW1505]

I will to contact the researcher for whom it was built tonight. Please PM with your contact info as the files will be a bit much for email. TopHat (1.4.1 and 1.3.3), as implemented in my port, requires 64-bit Samtools, 64-bit Bowtie, several supporting files, and does not do .gz compression.