Missing requirements about octopus

[dancooke]

Sure. Although these are really requirements of htslib rather than octopus per se. I'll update the docs for the next release in any case.

[jbedo]

You're right, it was only cmake that used these extra dependencies. Octopus compiled fine after this patch and without the extra dependencies.

rem-deps.patch.gz

[dancooke]

This patch causes a bunch of link errors if using htslib 1.4 or greater on OSX and Linux. In fact, I remember this is why I added these now in commits 5e50a22 and a0408c7.

[jbedo]

Sounds like a linking problem with your htslib, it should be linking in its dependencies implicitly. I'm using linux and my htslib v1.6 is appropriately linked. Could be some bugs possible if explicitly linking against a different version to what htslib is compiled against? Not sure.

[dancooke]

Do you recall how you installed htslib? I just installed the latest develop version manually and continue to encounter link errors when installing octopus without explicitly finding htslib's dependencies. I agree it's weird, and shouldn't be necessary.

[dancooke]

Although this guide on writing CMake find modules suggests library dependencies should explicitly be found themselves...

[jbedo]

Strange, what does ldd say on your library? I'm compiling using nix, which doesn't do anything special (the build expression is here). My ldd shows the library correctly linked against its dependencies:

[nix-shell:~]$ ldd /nix/store/cgj7cxnnl8jmp2qppsaxnrbwa57wv657-htslib-1.6/lib/libhts.so.2
ldd: warning: you do not have execution permission for `/nix/store/cgj7cxnnl8jmp2qppsaxnrbwa57wv657-htslib-1.6/lib/libhts.so.2'
        linux-vdso.so.1 (0x00007fff02bbc000)
        liblzma.so.5 => /nix/store/8b6gq3ay5i968i5jxzdk6x0jazxg508g-xz-5.2.3/lib/liblzma.so.5 (0x00007f175fdad000)
        libbz2.so.1 => /nix/store/m9fm5ls687zxwc2299acrw9i5k3vi0n8-bzip2-1.0.6.0.1/lib/libbz2.so.1 (0x00007f175fb9d000)
        libz.so.1 => /nix/store/qwihrwyc72qd57grhqmfzkvvpd8611yf-zlib-1.2.11/lib/libz.so.1 (0x00007f175f986000)
        libm.so.6 => /nix/store/9g2xkgiaqqzvajgb8d4hv5yqg2n96flr-glibc-2.26-75/lib/libm.so.6 (0x00007f175f63a000)
        libcurl.so.4 => /nix/store/78nh8kaacpcka6w6x0fpirlaxidyy0qa-curl-7.57.0/lib/libcurl.so.4 (0x00007f175f3bc000)
        libcrypto.so.1.0.0 => /nix/store/6dvn6wjy79yxsbz05sgcm8xplbidq5s6-openssl-1.0.2n/lib/libcrypto.so.1.0.0 (0x00007f175ef81000)
        libpthread.so.0 => /nix/store/9g2xkgiaqqzvajgb8d4hv5yqg2n96flr-glibc-2.26-75/lib/libpthread.so.0 (0x00007f175ed63000)
        libc.so.6 => /nix/store/9g2xkgiaqqzvajgb8d4hv5yqg2n96flr-glibc-2.26-75/lib/libc.so.6 (0x00007f175e9b0000)
        /nix/store/9g2xkgiaqqzvajgb8d4hv5yqg2n96flr-glibc-2.26-75/lib64/ld-linux-x86-64.so.2 (0x00007f1760280000)
        libnghttp2.so.14 => /nix/store/lc45jlqa3ra7y34nz148bmdiv8jaw0qm-nghttp2-1.24.0-lib/lib/libnghttp2.so.14 (0x00007f175e78a000)
        libssh2.so.1 => /nix/store/4plv316zazflkbnz1yv92il3v5sjjk2i-libssh2-1.8.0/lib/libssh2.so.1 (0x00007f175e55c000)
        libssl.so.1.0.0 => /nix/store/6dvn6wjy79yxsbz05sgcm8xplbidq5s6-openssl-1.0.2n/lib/libssl.so.1.0.0 (0x00007f175e2ee000)
        libdl.so.2 => /nix/store/9g2xkgiaqqzvajgb8d4hv5yqg2n96flr-glibc-2.26-75/lib/libdl.so.2 (0x00007f175e0ea000)

I also just tried compiling htslib quickly on a fresh ubuntu image (./configure && make) and that also seemed to link correctly:

root@7a77cbe15932:/tmp/htslib-1.6# ldd libhts.so
        linux-vdso.so.1 =>  (0x00007ffeb30ea000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f5c24c30000)
        libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f5c24a20000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f5c24806000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5c244fd000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5c242e0000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5c23f16000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f5c23d12000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f5c250fa000)

[dancooke]

Sorry for the delayed response. I found the problem. It was because on my system, the static htslib version (libhts.a) was being used, which requires dependencies be explicitly linked otherwise there are unresolved symbols. On your system, the dynamic version (libhts.so) was being selected, so no need to link the dependencies. I've modified the installation process to default to always find the dynamic version, in which case CMake won't try to find the dependencies. There is still the option to statically link (--static) command to install.py. These changes are available in v0.3.3-alpha.