Bedtools on Cygwin problem.

Question

[K.Nijbroek]

Hi

I'm trying to install the latest release of Bedtools via Cygwin but there's a weird error during process. I know this isn't the best solution, but I do not have an other choice. Perhaps anyone knows how to fix this?

NijbroekK@UTWKS11498 /cygdrive/g/Stage_Enschede/methods/methods_Bedtoolsnew
$ make clean
 * Cleaning-up BamTools API
 * Cleaning up.

NijbroekK@UTWKS11498 /cygdrive/g/Stage_Enschede/methods/methods_Bedtoolsnew
$ make
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.20.1
CURRENT_VERSION  = v2.20.1
 * Creating BamTools API
- Building in src/utils/bedFile
  * compiling bedFile.cpp
bedFile.cpp:1:0: warning: -fPIC ignored for target (all code is position independent) [enabled by default]
 /*****************************************************************************
 ^
- Building in src/utils/BinTree
  * compiling BinTree.cpp
BinTree.cpp:1:0: warning: -fPIC ignored for target (all code is position independent) [enabled by default]
 #include "BinTree.h"
 ^
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:16:0,
                 from ../../utils//FileRecordTools/FileRecordMgr.h:19,
                 from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11,
                 from ../../utils//Contexts/ContextBase.h:23,
                 from ../../utils//Contexts/ContextIntersect.h:11,
                 from BinTree.h:20,
                 from BinTree.cpp:1:
../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:16:27: fatal error: ../../utils//BamTools/include/api/BamReader.h: Permission denied
 #include "api/BamReader.h"
                           ^
compilation terminated.
Makefile:29: recipe for target '../../../obj//BinTree.o' failed
make[1]: *** [../../../obj//BinTree.o] Error 1
Makefile:130: recipe for target 'src/utils/BinTree' failed
make: *** [src/utils/BinTree] Error 2

NijbroekK@UTWKS11498 /cygdrive/g/Stage_Enschede/methods/methods_Bedtoolsnew
$

[Alex Reynolds]

If you need to manipulate BED files in Cygwin, BEDOPS compiles on 64-bit versions with the latest GCC as the compiler (http://bedops.readthedocs.org/en/latest/content/installation.html#cygwin). As an alternative to Cygwin, however, you could run a common Linux distribution within VirtualBox and set up your environment there.