CODEWITHSUNDEEP
cygwin
Bisan
Bisan

Reputation: 11

Error while installing bedtools via cygwin commands: fatal error: zlib.h: No such file or directory

I'm trying to install the bedtools v2.27.0 via Cygwin. Here are the commands I've tried:

$ wget https://github.com/arq5x/bedtools2/releases/download/v2.27.0/bedtools-2.27.0.tar.gz
$ tar -zxvf bedtools-2.27.0.tar.gz
$ cd bedtools2
$ make

when running the last command, I get the following error:

*fatal error: zlib.h: No such file or directory  
*#include <zlib.h>*  
^  
compilation terminated.  
make[1]: *** [Makefile:37: ../../../obj//FileRecordMgr.o] Error 1  
make: *** [Makefile:187: src/utils/FileRecordTools] Error 2*

I tried downloading the libz package using the following command:

$ apt-cyg install libz-dev

but it didn't work. I got the following error:

Unable to locate package libz-dev

Note that I'm using Cygwin terminal on windows (64-bit machine). Your help is highly appreciated.

Upvotes: 1

Views: 1979

Answers (1)

matzeri
matzeri

Reputation: 8496

To install packages use cygwin setup, or at least find the right package name before using apt-cyg

To find the package containing zlib.h header:

$ cygcheck -p include/zlib.h
Found 10 matches for include/zlib.h
...
zlib-devel-1.2.11-1 - zlib-devel: gzip de/compression library (development)
..

So you need to install zlib-devel

Upvotes: 2

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