help request for running SOAPdenovo

Question

[reza]

hi everyone

i downloaded program from here, http://soap.genomics.org.cn/soapdenovo.html. when i run "make" command in cygwin in c/users/rain/desktop/SOAPdenove2-src-r240 (my own soap directory in my PC) i get below error.

error: ‘usleep’ was not declared in this scope while ( io_ready == 0 ) {usleep ( 1 );}

inc/stdinc.h:33:17: fatal error: aio.h: No such file or directory

second question: after installing program what are steps of assembly running. i have manual of program but it confuse me. anybody can explain clearly soapdenovo running step by step for illumina paired end data?

Answer 1

[Sej Modha]

If you are using Cygwin then you can use the pre-compiled linux version of the software that is available to download from here.