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Old 06-11-2013, 12:03 AM   #1
lsantome
Junior Member
 
Location: Spain

Join Date: Feb 2013
Posts: 8
Default Newbie need help to install BEDTools under Cigwin

Hi all,

I've been trying to install BEDTools under Cigwin but I get the following error message in the last step:

$ make all
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.17.0
CURRENT_VERSION =
Updating version file.
* Creating BamTools API
- Building in src/utils/bedFile
* compiling bedFile.cpp
bedFile.cpp:1: warning: -fPIC ignored for target (all code is position independent)
In file included from bedFile.h:16,
from bedFile.cpp:12:
../../utils//gzstream/gzstream.h:35:18: zlib.h: No such file or directory
In file included from bedFile.h:16,
from bedFile.cpp:12:
../../utils//gzstream/gzstream.h:50: error: `gzFile' does not name a type
Makefile:22: recipe for target `../../../obj//bedFile.o' failed
make[1]: *** [../../../obj//bedFile.o] Error 1
Makefile:120: recipe for target `src/utils/bedFile' failed
make: *** [src/utils/bedFile] Error 2


I've previously installed BEDTools in a Ubuntu virtual machine without any problem, but it makes my desktop PC very slow.

I've apparently installed all the required packages for the installation under cigwin. I hope you can help me. I'd appreciate it a lot.

Thank you in advance
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Old 06-11-2013, 04:08 AM   #2
GenoMax
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Are you certain you have installed "zlib"? If not this may help: http://askubuntu.com/questions/21059...-using-apt-get
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Old 06-11-2013, 10:33 PM   #3
lsantome
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Default

Quote:
Originally Posted by GenoMax View Post
Are you certain you have installed "zlib"? If not this may help: http://askubuntu.com/questions/21059...-using-apt-get
Hi Genomax,

Thank you for your answer

After installing "zlib" and "libgcrypt" I got the same error

I'll keep trying it
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Old 03-15-2015, 04:42 AM   #4
bakerwm
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Location: China

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Default

Quote:
Originally Posted by lsantome View Post
Hi Genomax,

Thank you for your answer

After installing "zlib" and "libgcrypt" I got the same error

I'll keep trying it
Hi, Have you fixed this error yet?

I got the same warnings when install BEDtools under Cygwin (MobaXterm 7.6).

I also find an answer on Biostars, it may be helpful: https://www.biostars.org/p/103210/
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Old 03-16-2015, 01:45 AM   #5
jmarshall
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Location: Cambridge, UK

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If the error you get when building bedtools (or other software) is

Quote:
zlib.h: No such file or directory
then on Cygwin the package you need to ensure is installed is zlib-devel.
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