Announce samtools on Windows x64

[xied75]

Dear all,

samtools is up for download here:

http://bow.codeplex.com/

Source code is here:

https://github.com/xied75/samtools

Visual studio solution files to follow, in case you would like to compile it yourself.

Best,

Dong Xie

[maubp]

It is a shame you forked from the old experimental git repository https://github.com/lh3/samtools (which had a partial history only) instead of the official git repository https://github.com/samtools/samtools (converted from SVN) which would then make it much easier to submit a pull request to merge the code contributions.

However, looking over your repository, it looks like one big commit, a lot of which looks like white space changes which obscures the real work

https://github.com/xied75/samtools/commit/0726ba748e0556aa45de0e933dc98caeede9eec9

[xied75]

Gosh!

It's only yesterday LH said this: https://github.com/lh3/samtools/issu...omment-5720997

So someone please confirm WHICH is really official?!

In fact I started my coding from sourceforge http://sourceforge.net/projects/samt...mtools/0.1.18/

It's only because I need to release the source on GitHub thus I forked from lh3. I don't even know the other one before you said it.

And, this is a fork for 64 bit Windows, no, it's not just white space differences, can you use some diff tool options to ignore new-line or space diff (I use winmerge).

Most of the changes are done to work around the Microsoft Visual C++'s non-exist support of C99, except 1 or 2 places I may suggest a pull, I don't see any reason this fork need to be pull/merged with master branch.

To be clear, my fork doesn't need any 3rd party library to compile, and the output generated is identical with Linux version. I understand that inside samtools source there are some places mentioned Windows/Win32, yet these code only help you compile a .exe under some 3rd party library, but that binary is useless for serious work.

One thing I did test is pipe, pipe in pipe out, so you can chain samtools.exe like you can on Linux, e.g. samtools view -bSu toy.sam | samtools sort -n -o - nsort_tmp | samtools fixmate - - | samtools sort -o - csort_tmp | samtools fillmd -u - ref.fa > fixed_bam.bam
(note: this is a step in 1000G project data process, my windows version generates identical output as Linux, on similar speed.)

Best,

dong

[maubp]

The repository situation is not so clear unless you've been following on the samtools-devel mailing list. There are still some out of date references to SVN on the main http://samtools.sourceforge.net/ homepage

It seems to me that any changes to get samtools to compile on Windows 64 bit should go into the main repository, just like changes to get it to compile on Windows 32 bit, with suitable #defines.

As regards testing, see open issue https://github.com/samtools/samtools/issues/1

[xied75]

After two weeks radio silence, I found the download number on my codeplex interesting, 47 times of BWA x64 v.s. 16 times of samtools x64. Leave me wonder how come people only want BWA without using samtools?!

So I thought it's better to make some statements here, which Peter might also agree.

1, Above discussions are about some technique details of source code control system, and some unsettled issues within a certain small circle.
2, In no way item 1 affects my code/work quality and the usability of my port, or my good intention.
3, Thus if you are regular end user who run Windows and need samtools, you can safely skip above discussions and download my port to try out.

Best,

dong

[honey]

Suggestion

My one cent suggestion is if you can enlist steps (in the form of a link) to download and head start using BWA and samtools for biologist that will be useful. Consider other people are computer illiterate. Just as Jon Kates in this forum has done.

[xied75]

... I was trying to say the download number is unbalanced on my codeplex site ... that is more download on bwa than samtools ...

Anyway, I only recently realized that most Windows users are expecting tools with easy accessable GUI and prefer mouse click than command line terminal. This is definitely different than the Linux way.

I can't do much to change the bwa and samtools into Windows style because these were designed with Unix spirit. What I can do is wrap these tools into GUI so that Windows user could click mouse, just not sure how many would prefer this.

Could you show me the threads by Jon Kates? My search on this name got no results.

I might able to document how you use these tools under Windows, step by step, or with screen capture, if there is demand. (p.s. If you want something like that, please shout!)

Best,

dong

[honey]

Info

sorry about name typo-

http://seqanswers.com/forums/showthread.php?t=4589&highlight=circos

I understand your point however what I what to point out that adding steps will be kind of easy to follow by biologist. It is not for me personally but for the scientific community here especially biologists without depending upon bioinfromatic personnel. The simplest way may be if you just put down the steps as in attached post (may be without GUI) that may be very helpful.

Thanks

[mathew]

samtools and BWA for windows

I think such detiled steps to instalation and getting started with BWA and samtools in windows environment should be useful.
Thanks

[Collidor]

Has anyone experienced issues trying to run samtools on windows x64? The .exe files don't seem to launch properly on my machine.
Best,
J

[Richard Finney]

Anybody tried samtools 1.1 wih modern Visual C compiler on windows lately?

Any suggestions ?

[serhatg]

Anybody tried samtools 1.1 wih modern Visual C compiler on windows lately?

Any suggestions ?

Hi @Richard, I am also trying to compile the source with Visual Studio.I am just wondering if you managed to compile it ?

Thanks,
Serhat

[Richard Finney]

It's a pain porting to visual C.

I ~tried~. I got hung up chasing the thread stuff after 0.19 samtools and never punched it through.

I do have a hacked Visual C samtools 0.18 available at NCI's Alview github site https://github.com/NCIP/alview under sam01832 directory; however full functionality might not be not there. I just needed the darn bam read capability and did not test other features.

Heng went a little wild on the khash table stuff which makes it very tough to cut out just a chunk of samtools.

[serhatg]

Thanks a lot! I will check it out. I have asked @Dong for the solution files as it would be much more easier to move on with.

Cheers,
Serhat

[jvolanen]

Hi @Richard, I am also trying to compile the source with Visual Studio.I am just wondering if you managed to compile it ?

Thanks,
Serhat

We managed to compile samtools 1.1 on Windows (64 bit). Most of the functionality works. If you are interested, omnomicsQ contains compiled samtools which you can use. A registration for a free trial is needed.

We are planning to submit the modifications to github in the near future.

Best regards
Jussi