How to work with clustalw source code?

Question

[TJay]

Hi,

I'm trying to do some changes with the clustalw source code.I'm using Windows 8.1 and i installed MinGW with MSYS. But i was not able to run the main.cpp as there were some errors from that file. I tried from visual studio too. Same thing happen to me. So can some one explain the way to run this source code?

[Michael]

How did you try to compile that, your error report is not precise enough either.

[TJay]

In command prompt, the command and the error is as follows.

D:\clustalw-2.1\clustalw-2.1\src>g++ -o m main.cpp

In file included from interface/InteractiveMenu.h:15:0, from main.cpp:17: interface/../Clustal.h:15:22: fatal error: clustalw.h: No such file or directory #include "clustalw.h" ^ compilation terminated.

[Pierre Lindenbaum]

this is is the right way to run g++/gcc , but for VERY simple programs.

For complex program you need to add the path to the include files, the multiple source, preprocessing directives, some linking directives, etc... I suppose clustal comes with a Makefile. You'd better use this instead of trying to compile this by yourself.

[Michael]

Yep, use the makefile, also you need Cygwin, is it installed?

[TJay]

Yes.I installed Cygwin and run ./configure and then make command. After run make command i got some errors as,

./general/Stats.cpp: In member function 'void clustalw::Stats::logInputSeqStats(clustalw::Alignment*)': ./general/Stats.cpp:269:25: error: 'time' was not declared in this scope time_t t = time(NULL); ^ ./general/Stats.cpp:270:25: error: 'localtime' was not declared in this scope tm s = *localtime(&t); ^ ./general/Stats.cpp:281:90: error: 'asctime' was not declared in this scope fprintf(fp, "logging job: %s on %s", userParameters->getSeqName().c_str(), asctime(&s)); ^

make[3]: * [Stats.o] Error 1

make[3]: Leaving directory `/d/clustalw-2.1/clustalw-2.1/src'

make[2]: * [all-recursive] Error 1

make[2]: Leaving directory `/d/clustalw-2.1/clustalw-2.1/src'

make[1]: * [all] Error 2

make[1]: Leaving directory `/d/clustalw-2.1/clustalw-2.1/src'

make: * [all-recursive] Error 1

I attached a snapshot of Cygwin window.

[Pierre Lindenbaum]

in Stats.cpp include the following line at the top of the file:

#include <ctime>

[TJay]

That's the problem. Thank you so much..