07-16-2012
You need faToTwoBit compiled in Windows exe (PE) format but against cygwin1.dll not the native windows dll. You can't run native ELF binaries on Cygwin.
As fas as I know, the faToTwoBit application hasn't been ported yet to cygwin.
You can take a look here:
samtools installation - SEQanswers
SAMtools installation - SEQanswers
Seems to be problematic to compile under cygwin.
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LEARN ABOUT MOJAVE
inline-support
Inline-Support(3) User Contributed Perl Documentation Inline-Support(3)
NAME
Inline-Support - Support Information for Inline.pm and related modules.
DESCRIPTION
This document contains all of the latest support information for "Inline.pm" and the recognized Inline Language Support Modules (ILSMs)
available on CPAN.
SUPPORTED LANGUAGES
The most important language that Inline supports is "C". That is because Perl itself is written in "C". By giving a your Perl scripts
access to "C", you in effect give them access to the entire glorious internals of Perl. (Caveat scriptor :-)
As of this writing, Inline also supports:
- C++
- Java
- Python
- Tcl
- Assembly
- CPR
- And even Inline::Foo! :)
Projects that I would most like to see happen in the year 2001 are:
- Fortran
- Ruby
- Lisp
- Guile
- Bash
- Perl4
SUPPORTED PLATFORMS
"Inline::C" should work anywhere that CPAN extension modules (those that use XS) can be installed, using the typical install format of:
perl Makefile.PL
make
make test
make install
It has been tested on many Unix and Windows variants.
NOTE: "Inline::C" requires Perl 5.005 or higher because "Parse::RecDescent" requires it. (Something to do with the "qr" operator)
Inline has been successfully tested at one time or another on the following platforms:
Linux
Solaris
SunOS
HPUX
AIX
FreeBSD
OpenBSD
BeOS
OS X
WinNT
Win2K
WinME
Win98
Cygwin
The Microsoft tests deserve a little more explanation. I used the following:
Windows NT 4.0 (service pack 6)
Perl 5.005_03 (ActiveState build 522)
MS Visual C++ 6.0
The "nmake" make utility (distributed w/ Visual C++)
"Inline::C" pulls all of its base configuration (including which "make" utility to use) from "Config.pm". Since your MSWin32 version of
Perl probably came from ActiveState (as a binary distribution) the "Config.pm" will indicate that "nmake" is the system's "make" utility.
That is because ActiveState uses Visual C++ to compile Perl.
To install "Inline.pm" (or any other CPAN module) on MSWin32 w/ Visual C++, use these:
perl Makefile.PL
nmake
nmake test
nmake install
Inline has also been made to work with Mingw32/gcc on all Windows platforms. This is a free compiler for Windows. You must also use a perl
built with that compiler.
The "Cygwin" test was done on a Windows 98 machine using the Cygwin Unix/Win32 porting layer software from Cygnus. The "perl" binary on
this machine was also compiled using the Cygwin tool set ("gcc"). This software is freely available from http://sources.redhat.com/cygwin/
If you get Inline to work on a new platform, please send me email email. If it doesn't work, let me know as well and I'll see what can be
done.
SEE ALSO
For general information about Inline see Inline.
For information about using Inline with C see Inline::C.
For sample programs using Inline with C see Inline::C-Cookbook.
For information on writing your own Inline Language Support Module, see Inline-API.
Inline's mailing list is inline@perl.org
To subscribe, send email to inline-subscribe@perl.org
AUTHOR
Brian Ingerson <INGY@cpan.org>
COPYRIGHT
Copyright (c) 2000-2002. Brian Ingerson.
Copyright (c) 2008, 2010, 2011. Sisyphus.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
See http://www.perl.com/perl/misc/Artistic.html
perl v5.18.2 2012-11-19 Inline-Support(3)