Installing Bedtools with Cygwin fails.

Question

[omer.k]

I haven't been able to properly install bedtools with Cygwin (Win 7), base off of the native instructions. I searched online and found that it might be usefull to reinstall Cygwin with a few extra packages. I've done so and re-attempted make clean, and then make, but no cigar. I re-run make > SaveOutputToFile.txt File content is attached.

How could I fix this?

Building BEDTools:
=========================================================
DETECTED_VERSION = v2.27.0
CURRENT_VERSION  = 
Updating version file.
 * Creating BamTools API
- Building in src/utils/FileRecordTools
  * compiling FileRecordMgr.cpp
  * compiling FileRecordMergeMgr.cpp
- Building in FileReaders
  * compiling FileReader.cpp
  * compiling SingleLineDelimTextFileReader.cpp
  * compiling BamFileReader.cpp
  * compiling BufferedStreamMgr.cpp
  * compiling InputStreamMgr.cpp
- Building in Records
  * compiling Record.cpp
  * compiling EmptyRecord.cpp
  * compiling Bed3Interval.cpp
  * compiling Bed4Interval.cpp
  * compiling BedGraphInterval.cpp
  * compiling Bed5Interval.cpp
  * compiling Bed6Interval.cpp
  * compiling PlusFields.cpp
  * compiling BedPlusInterval.cpp
  * compiling Bed12Interval.cpp
  * compiling BamRecord.cpp
  * compiling GffRecord.cpp
  * compiling GffPlusRecord.cpp
  * compiling VcfRecord.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling BlockMgr.cpp
  * compiling StrandQueue.cpp
  * compiling RecordMgr.cpp
  * compiling RecordList.cpp
  * compiling RecordKeyList.cpp
  * compiling RecordKeyVector.cpp
- Building in src/utils/FileRecordTools/FileReaders
make[1]: Nothing to be done for 'all'.
- Building in src/utils/FileRecordTools/Records
make[1]: Nothing to be done for 'all'.
- Building in src/utils/bedFile
  * compiling bedFile.cpp
- Building in src/utils/BinTree
  * compiling BinTree.cpp
- Building in src/utils/version
  * compiling version.cpp
- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
  * compiling chromsweep.cpp
- Building in src/utils/Contexts
  * compiling ContextBase.cpp
Makefile:38: recipe for target '../../../obj//ContextBase.o' failed
Makefile:186: recipe for target 'src/utils/Contexts' failed

[h.mon]

Questions about Cygwin install issues come up from time to time, but most remain unanswered, because there aren't many people doing bioinformatics with Cygwin. My advice is you should try something else, such as a virtual machine or install Linux alongside Windows.

[omer.k]

Thanks, will consider, but this is what I have to work with currently. Still hoping someone encountered and troubleshooted through this problem.

Answer 1

[Jorge Amigo]

After being stuck for years at version v2.26.0 on a Windows machine I sometimes have to work with, I've recently came across this github project which actually solved this issue.

It currently contains a Cygwin compilable version of bedtools v2.29.2, which is not the latest, but if you compare the differences with the main branch you'll see that it's only a matter of changing the compiler in the Makefile, adding 2 .h function files (which you can grab from that modified v2.29.2 tar.gz file), and adding 1 line of code to 3 files, so applying those same changes over the master branch allows you to have latest bedtools version working on Cygwin:

$ cygcheck -V
cygcheck (cygwin) 3.2.0
System Checker for Cygwin
Copyright (C) 1998 - 2021 Cygwin Authors
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ bedtools.exe --version
bedtools v2.30.0

[jared.andrews07]

Alternatively, the Windows Subsystem for Linux is quite mature at this point and has no trouble with bedtools (or most other bioinformatics tools).