Integrating HapCUT2

[tarini92]

While trying to run extractHAIRS and HAPCUT2 for getting haplotype phasing outputs, I cloned the HAPCUT2 and got the following error while making it from source.

git submodule init
Submodule 'submodules/htslib' (https://github.com/samtools/htslib) registered for path 'submodules/htslib'
Submodule 'submodules/samtools' (https://github.com/samtools/samtools) registered for path 'submodules/samtools'
git submodule update
Cloning into 'submodules/htslib'...
remote: Enumerating objects: 51, done.
remote: Counting objects: 100% (51/51), done.
remote: Compressing objects: 100% (30/30), done.
remote: Total 10677 (delta 25), reused 32 (delta 21), pack-reused 10626
Receiving objects: 100% (10677/10677), 8.10 MiB | 0 bytes/s, done.
Resolving deltas: 100% (7452/7452), done.
Checking connectivity... done.
Submodule path 'submodules/htslib': checked out '26229a368e3045a827f04fc03f3879e25f110ba3'
Cloning into 'submodules/samtools'...
remote: Enumerating objects: 26, done.
remote: Counting objects: 100% (26/26), done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 9954 (delta 10), reused 10 (delta 5), pack-reused 9928
Receiving objects: 100% (9954/9954), 11.44 MiB | 0 bytes/s, done.
Resolving deltas: 100% (6468/6468), done.
Checking connectivity... done.
Submodule path 'submodules/samtools': checked out '255f97daffd3a27d7b063e991a993f47ad6186cf'
echo "Building Samtools bam library..."
Building Samtools bam library...
make -C submodules/samtools lib
make[1]: Entering directory '/home/jupyter/notebooks/HapCUT2/submodules/samtools'
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I../htslib -c -o bam_aux.o bam_aux.c
In file included from bam.h:48:0,
                 from bam_aux.c:27:
../htslib/htslib/bgzf.h:34:18: fatal error: zlib.h: No such file or directory
compilation terminated.
Makefile:116: recipe for target 'bam_aux.o' failed
make[1]: *** [bam_aux.o] Error 1
make[1]: Leaving directory '/home/jupyter/notebooks/HapCUT2/submodules/samtools'
Makefile:32: recipe for target 'submodules/samtools/libbam.a' failed
make: *** [submodules/samtools/libbam.a] Error 2
root@92c193bba70f:~/notebooks/HapCUT2# make install-hairs
cp build/extractHAIRS /usr/local/bin
cp: cannot stat 'build/extractHAIRS': No such file or directory
Makefile:95: recipe for target 'install-hairs' failed
make: *** [install-hairs] Error 1

How can I integrate HAPCUT with neoepiscope without running into these errors?

[maryawood]

Hi there,

I can't speak from experience because I haven't run into this problem when trying to build HapCUT2. That said, I googled your error, and came across this Stack Overflow page:

https://stackoverflow.com/questions/36374267/how-to-fix-fatal-error-zlib-h-no-such-file-or-directory?rq=1

Maybe you need to install the development support files for zlib as described by the top answer? If that doesn't help, you might want to create a new issue on the HapCUT2 repo, as the developers there may have a better idea about what's going on:

https://github.com/vibansal/HapCUT2/issues

If you're unable to solve the problems with HapCUT2, I'm happy to help you set up a work flow using GATK's ReadBackedPhasing for variant phasing instead of HapCUT2!

[tarini92]

Hi,

Thanks, installing a variant of zlib using apt-get worked.