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Top Forums Shell Programming and Scripting Cygwin - cannot execute binary file Post 302672451 by Tribe on Monday 16th of July 2012 11:14:39 AM
Old 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.
This User Gave Thanks to Tribe For This Post:
 

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File::Spec::Cygwin(3pm) 				 Perl Programmers Reference Guide				   File::Spec::Cygwin(3pm)

NAME
File::Spec::Cygwin - methods for Cygwin file specs SYNOPSIS
require File::Spec::Cygwin; # Done internally by File::Spec if needed DESCRIPTION
See File::Spec and File::Spec::Unix. This package overrides the implementation of these methods, not the semantics. This module is still in beta. Cygwin-knowledgeable folks are invited to offer patches and suggestions. canonpath Any "" (backslashes) are converted to "/" (forward slashes), and then File::Spec::Unix canonpath() is called on the result. file_name_is_absolute True is returned if the file name begins with "drive_letter:", and if not, File::Spec::Unix file_name_is_absolute() is called. tmpdir (override) Returns a string representation of the first existing directory from the following list: $ENV{TMPDIR} /tmp $ENV{'TMP'} $ENV{'TEMP'} C:/temp Since Perl 5.8.0, if running under taint mode, and if the environment variables are tainted, they are not used. case_tolerant Override Unix. Cygwin case-tolerance depends on managed mount settings and as with MsWin32 on GetVolumeInformation() $ouFsFlags == FS_CASE_SENSITIVE, indicating the case significance when comparing file specifications. Default: 1 COPYRIGHT
Copyright (c) 2004,2007 by the Perl 5 Porters. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.12.1 2010-04-27 File::Spec::Cygwin(3pm)
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