[EMBOSS] How to compile water.c

[Jon Ison]

Hi Justin

You might be better off using the native windows code for EMBOSS developed
by Alan Bleasby - which I don't think is available via our website yet but
Alan can provide.  Feel free to email emboss-bug about it.

Cheers

Jon


> Justin, 3 days ago I have been try in struggling with this problem.
>
> If you have MSDN installed on your computer see in it contents explorer:
>
> *	Win32 and COM Development
> o	Development Guides
> *	UNIX Application Migration Guide
> *	Chapter 9: Win32 Code Conversion
>
> Or go on link:
> http://search.microsoft.com/results.aspx?mkt=en-US&setlang=en-US&q=Overview+o
> f+the+UNIX+Application+Migration+Guide
>
> If you make a decision to port header files, you must be convert all UNIX
> scecifics:
>  - UNIX creates a new process by using fork
>  - converting UNIX code to Win32 requires the use of new techniques replacing
> the use of some UNIX signals
>  - specific in working with threads
>  - synchronization issues
>  - specific in users, groups and security management
>  - specific in file and data access management
>  - an so on.
>
> Also, you must come to know the particulars of some header files, absent in
> Win32, i.e.:
>  - dirent.h
>  - dirent_w32.h
>  - win32.h
>  - <pwd.h>
>  - <sys/wait.h>
>  - and some else
>
>
> Regards, Nick.
>
> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org
> [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of john p
> Sent: Friday, April 13, 2007 8:28 AM
> To: emboss at lists.open-bio.org
> Subject: [EMBOSS] How to compile water.c
>
> Greeting wise ones,,
>
> My name is Justin from Malaysia. I've just started a postgrad research on
> accelerating bioinformatics applications.
>
> My current task is to analyze and profile the smith-waterman algorithm. I
> dont have much experience on C programming and am just picking up. I need to
> compile water.c in Win XP. I'm currently using Visual Studio C++ Express and
> Dev-C++.
>
> When trying to compile water.c, i encountered many problems... they were a
> lot of linking errors and stuff... Plus i need to enable profiling info
> (gmon.out) so that i can profile it using gprof.
> Maybe i got off to a bad start.. so i want to try again properly.
>
> Could you give me some guide/intructions on how to compile water.c? and where
> do i find the complete list of header and function files needed to compile
> with water.c?
>
> Please advise.
>
> Justin
>
>
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