Any chance of updating the bioconda recipe to 0.6.3-beta? about octopus

[rspreafico-vir]

Now available!

bioconda/bioconda-recipes#18935

[dancooke]

Thanks for your interest in Octopus. I've been trying to get the Bioconda version bumped for a while now but there are some issues with the new Bioconda Boost package. I'll ping the Bioconda team another message.

By the way, depending on your system, Octopus can run substantially faster when compiled from source on the target machine compare with the Bioconda version.

[tfenne]

Thanks @dancooke that's good to know. I'm currently building from source after installing all dependencies via conda, and that works well now that I have it scripted.

[rspreafico-vir]

@dancooke I have a PR open with bioconda to build octopus 0.6.3 that worked successfully on Linux, but not on Mac:

bioconda/bioconda-recipes#18935

boost seems to be recognized on Mac, the issue now is htslib:

21:55:56 BIOCONDA INFO (ERR) -- Installation prefix: /Users/distiller/project/miniconda/conda-bld/octopus_1574833993285/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin
21:55:58 BIOCONDA INFO (ERR) HTSlib_INCLUDE_DIR=HTSlib_INCLUDE_DIR-NOTFOUND
21:55:58 BIOCONDA INFO (ERR) HTSlib_LIBRARY=/Users/distiller/project/miniconda/conda-bld/octopus_1574833993285/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/libhts.dylib
21:55:58 BIOCONDA INFO (ERR) CMake Error at build/cmake/modules/FindHTSlib.cmake:67 (message):
21:55:58 BIOCONDA INFO (ERR)   Required library HTSlib NOT FOUND.
21:55:58 BIOCONDA INFO (ERR) 
21:55:58 BIOCONDA INFO (ERR)   Install the library (dev version) and try again.  If the library is already
21:55:58 BIOCONDA INFO (ERR)   installed, use ccmake to set the missing variables manually.
21:55:58 BIOCONDA INFO (ERR) Call Stack (most recent call first):
21:55:58 BIOCONDA INFO (ERR)   build/cmake/modules/FindHTSlib.cmake:144 (libfind_process)
21:55:58 BIOCONDA INFO (ERR)   src/CMakeLists.txt:692 (find_package)

Do you have any idea on how to solve this? I will also ping the Bioconda crew.

[dancooke]

@rspreafico-vir Thanks!