HISAT2 Windows Binaries

There is an unordinate shortness of tools for running RNA-seq analysis on Windows. Most developers produce the sorurce code and make binaries for several Linux distributions and other flavors of Unix such as Mac OSX. The source code is many times available but the compilation of complex packages requiring several Unix and POSIX libraries is far from trivial in a non-POSIX system as MS Windows. Sometimes successful builds involve tweaking with the source code which is not for the faint hearted. Also many times the process is not reproducible, because a new version of s library suddenly becomes available and the "tweak" suddenly no longer works.

Thankfully the situation is changing with several tools becoming available for 64bit versions of Windows. Namely GeneCodes makes availableSAMTools, BWA, BowTie, GMAP-GSNAP and cufflinks. But one notorious absence is a reliable build of a more common spliced aligner. Although GSNAP is a possible choice, other tools as TopHat or STAR are much more popular. However, TopHat is notoriously difficult to build on Windows but it may be irrelevant soon as this tool is being superseeded by other tools as STAR and HISAT2

Compiling STAR on Windows is not easy and so far I have not been able to accomplish it. On the other hand HISAT2 is reported to be compilable on Windows under mingw32 or mingw64. Again, so far I have not been able to do it, even installing all recommended libraries and MSYS. Nonetheless, I was able to make a full HISAT2 build (version 2.0.4) under cygwin64 It required the installation of pthreads, zlib, boost and other libraries, but after the cygwin installation was completed, running make compiled all source files and produced the necessary executables.

In the hope that this tool might be useful to others running Windows, I make it available so that people may not have to go through the whole try and fail process. I have tested it under Windows 7 and Windows 10 (both 64 bits) and so far it has worked perfectly and integrated flawessly with SAMtools and cufflinks.

Please note: I GIVE NO WARRANTIES. I PROVIDE THE EXE FILES IN THE HOPE THEY MIGHT BE USEFUL. THIS SOFTWARE IS PROVIDED "AS IS" WITH NO WARRANTIES WHATSOEVER.

Although the produced binaries have so far worked perfectly, the recommended way to run HISAT2 is through the provided PERL script. To run the hisat2.pl script it is necessary to have a valid PERL installation. The last version of Strawberry PERL has worked with the present script with no noticeable issues.