undefined reference to `gzopen64'

[samtools]

undefined reference to `gzopen64'

[valeriuo]

Can you try the tabix shipped with htslib? There is not much work going around this repo.

[daviesrob]

Maybe we should add a README file saying "use HTSlib for an up-to-date version".

[jmarshall]

The repository description has a note, but it's easily missed.

Maybe the C source code should be deleted at this point, leaving only the Perl and Python wrapper modules in this repository?

(Sadly for the OP, I expect the same thing will happen when building HTSlib. They probably have another zlib installed as well as the system one, and htslib will react in much the same way. BTW -H needs to be added to the compiler commands, not just the final link command.)

[AGI-chandler]

Hi, thanks for your responses. I was following the instructions for Augustus/bam2wig which recommended this repo for tabix, https://github.com/Gaius-Augustus/Augustus/tree/master/auxprogs/bam2wig
I did get htslib-1.9 compiled and installed which did install tabix 1.9 into /usr/local/bin, so I guess this repo and installation of tabix is not needed?

[AGI-chandler]

It's true, I did just modify https://github.com/Gaius-Augustus/Augustus/blob/c23440b630a1af0b7c908cedc6e2d6e0e063c2a9/auxprogs/bam2wig/Makefile#L21 to TABIX=$(TOOLDIR)/htslib-1.9/ and was able to compile bam2wig. I could file an issue in the Augustus repo with this updated information for compilation?

And yes we have newer zlib installed locally for a while now but so far have not had issues with this.

[root@pac local]# ldd /usr/local/bin/tabix
	linux-vdso.so.1 =>  (0x00007fffd53e9000)
	liblzma.so.0 => /usr/lib64/liblzma.so.0 (0x00000030ad600000)
	libbz2.so.1 => /lib64/libbz2.so.1 (0x00000030b2e00000)
	** libz.so.1 => /usr/local/lib/libz.so.1 (0x00007f4d3a36c000) **
	libm.so.6 => /lib64/libm.so.6 (0x00000030a7a00000)
	libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x000000341a800000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x00000030a7e00000)
	libc.so.6 => /lib64/libc.so.6 (0x00000030a7600000)
	libidn.so.11 => /lib64/libidn.so.11 (0x00000030aaa00000)
	libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x000000341a000000)
	librt.so.1 => /lib64/librt.so.1 (0x00000030a8a00000)
	libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00000030abe00000)
	libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00000030ab600000)
	libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00000030ac600000)
	libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007f4d3a164000)
	libssl3.so => /usr/lib64/libssl3.so (0x0000003417c00000)
	libsmime3.so => /usr/lib64/libsmime3.so (0x00000030b1e00000)
	libnss3.so => /usr/lib64/libnss3.so (0x00000030afe00000)
	libnssutil3.so => /usr/lib64/libnssutil3.so (0x00000030b0200000)
	libplds4.so => /lib64/libplds4.so (0x00000030af200000)
	libplc4.so => /lib64/libplc4.so (0x00000030aee00000)
	libnspr4.so => /lib64/libnspr4.so (0x00000030af600000)
	libdl.so.2 => /lib64/libdl.so.2 (0x00000030a8200000)
	libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x000000341a400000)
	/lib64/ld-linux-x86-64.so.2 (0x00000030a7200000)
	liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x0000003418800000)
	libresolv.so.2 => /lib64/libresolv.so.2 (0x00000030a9600000)
	libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x00000030b1a00000)
	libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00000030aba00000)
	libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00000030ade00000)
	libssl.so.10 => /usr/lib64/libssl.so.10 (0x0000003417400000)
	libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x0000003416c00000)
	libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00000030ada00000)
	libselinux.so.1 => /lib64/libselinux.so.1 (0x00000030a8e00000)
	libfreebl3.so => /lib64/libfreebl3.so (0x00000030ad200000)

[root@pac local]# tabix --version
tabix (htslib) 1.9
Copyright (C) 2018 Genome Research Ltd.

[valeriuo]

I did get htslib-1.9 compiled and installed which did install tabix 1.9 into /usr/local/bin, so I guess this repo and installation of tabix is not needed?

Great! Yes, the tabix coming with htslib is the only maintained version.

I could file an issue in the Augustus repo with this updated information for compilation?

Yes, you should tell them to updated their build script and README.