BWA under 64-bit Windows?

[RDW]

Has anyone built BWA for 64-bit Windows? No problems under Linux or (32-bit) Cygwin, but MinGW-w64 is choking with:

In file included from bwtaln.c:12:0:
bwtgap.h:8:2: error: expected specifier-qualifier-list before 'u_int32_t'
make: *** [bwtaln.o] Error 1

Any ideas?

[mrawlins]

That looks like your stdint.h standard header may not be properly configured (which comes with your C compiler). Also, shouldn't it be uint32_t, not u_int32_t? Unless bwt defines the u_int32_t type I think that could be a typo.

[RDW]

Thanks for the reply. The BWA source uses both uint32_t and u_int32_t, sometimes in the same file. Looks like uint32_t is the preferred C99 version, and stdint.h defines this. I don't have any MinGW-w64 header that defines u_int32_t in my current environment, but it is defined in Cygwin's types.h, which may explain why I can build BWA there.

[RDW]

Well, fixed that one by adding a typedef to one of the headers. Some other issues were solved easily (added zlib and pthreads to the mingw library, had to run ranlib manually on libbwtgen.a, etc.), but I now see that mingw is missing POSIX stuff used by BWA like sys/resource.h, as well as drand48 and cousins. Looks like BWA would have to be ported rather than just recompiled for Win64.

[mfursov]

This project provides BWA tool for Windows:

http://ugene.unipro.ru/external.html

[RDW]

The UGENE version is still 32-bit, but they built it without Cygwin dependencies, which is promising for a 64-bit build. Might be worth re-visiting this.

[RDW]

I see that the Ugene guys have now added a 64-bit Windows build of BWA 0.5.9 to the external tools package mentioned above:

http://ugene.unipro.ru/downloads/ext_tools_win_64-bit.zip

[xied75]

Dear all,

Please check http://bow.codeplex.com/
Just released BWA on x64 Windows, natively compiled on Windows without using any 3dr party library.

Best,

dong

[RDW]

Please check http://bow.codeplex.com/
Just released BWA on x64 Windows, natively compiled on Windows without using any 3dr party library.

It looks like the licence for this build needs to be fixed. BWA is GPL3, but you are required to agree to the (GPL-incompatible) Microsoft Public Licence to download it.

[xied75]

Hi,

Yes I did think of that too. BWA source is under GPLv3 and MIT. Trouble is I don't know how to setup separate licenses for each of the tool I do, because I only intended to have just a single project under codeplex. And codeplex provides GPLv2, MIT, etc., no v3.

I could change the settings now, but I guess it's only a temp solution, would like someone good at licensing to give some idea.

Best,

dong

[RDW]

Hi Dong, I'm not familiar with Codeplex - is it compulsory to have a clickthrough licence, or could you turn this feature off? You could comply with the GPL just by including the source in your zip file (or a 'written offer' to supply it - but the source is so small it's easier to bundle it). You should probably be doing this anyway, as it's not obvious where to get the source at the moment. The original source archive contains a copy of the GPL. If you had to modify the source to build it under Windows, include this version - I'd be interested in how you got it to build!

[xied75]

Well, Codeplex is like other code share site I guess. I'm offered a list of different licenses, seems must choose one.

Regarding clickthrough license, once I went to a seminar on cloud computing, one of the speaker is both a lawyer and IT pro. When someone asked does he ever read the clickthrough licenses displayed by all kinds of websites, he simply answered 'no', and the reason is, 'reading license is something to do in work time and should be paid for'.

About the source code, I'm planned to put that online later, because, I need time to do clean up, double check all my fix, and prepare either a solution file or msbuild file, that all takes a lot time. And, to make this build, you also need to build zlib from source (I didn't just grab the lib/dll because I prefered a single container.) Believe me it's not that easy if you are not using MingW or Cygwin or whatever younameit.

Right now I'm busy on Windows Specific version of BWA (e.g. change BWA SAMPE to multithreading, etc.) and also SAMTOOLS. So time is really tight, how about you just download a BWA tar from BWA site and keep with this .exe?

Best,

dong

[RDW]

Yes, clickthroughs are probably as legally enforceable as this:

http://xkcd.com/501/

Right now I'm busy on Windows Specific version of BWA (e.g. change BWA SAMPE to multithreading, etc.) and also SAMTOOLS.

Sounds interesting - a lot of people would find this useful!

So time is really tight, how about you just download a BWA tar from BWA site and keep with this .exe?

Well, this doesn't affect me personally (I use BWA under Linux right now, and only brought this up because the original clickthrough MS licence jumped out at me), but if you've modified the source to make it build under Windows, then I think the licence experts would tell you that you need to make the modifications available to anyone who downloads your binary (just linking to the original tar wouldn't be enough to comply with the GPL).

[arvid]

License issue still not solved, and source code still not available

Well, Codeplex is like other code share site I guess. I'm offered a list of different licenses, seems must choose one.

Regarding clickthrough license, once I went to a seminar on cloud computing, one of the speaker is both a lawyer and IT pro. When someone asked does he ever read the clickthrough licenses displayed by all kinds of websites, he simply answered 'no', and the reason is, 'reading license is something to do in work time and should be paid for'.

About the source code, I'm planned to put that online later, because, I need time to do clean up, double check all my fix, and prepare either a solution file or msbuild file, that all takes a lot time. And, to make this build, you also need to build zlib from source (I didn't just grab the lib/dll because I prefered a single container.) Believe me it's not that easy if you are not using MingW or Cygwin or whatever younameit.

Right now I'm busy on Windows Specific version of BWA (e.g. change BWA SAMPE to multithreading, etc.) and also SAMTOOLS. So time is really tight, how about you just download a BWA tar from BWA site and keep with this .exe?

Best,

dong

While I agree that your build sounds like a great thing for Windows users (and I have some collaborators that would like to use it), I noticed that BOW on CodePlex is still licensed under the GPLv2, and none of your modified source code is available for download together with the binaries - both issues clear violations to the GPLv3. You cannot excuse yourself with the lack of time - then simply wait to distribute it until you do it properly - or ask others to give you a hand. And a reference to simply download the original source code (without your modifications) isn't compliant either.

Eventually you will need to skip CodePlex since they don't support GPLv3. Why not do it straight from the start and make the code available now (e.g. on SourceForge) so others may help out in improving the code you are working on?

Since I don't want to make myself liable, I cannot distribute your BWA fork to others - which I wanted to do in the first place. In this way, it will not be successfully disseminated in the community...

[xied75]

I know this licensing stuff will chase me, but didn't realize this fast.

I've contacted codeplex to ask them for a customer license display, i.e. GPLv3. See how it goes,

BTW, I have a question, inside BWA source, many files come with MIT, how does these two work together? And when you use many MIT files, you can still release code with GPLv3? (Forgive me for these simple questions maybe.)

Best,

dong