Installation problem

[natasacirovic]

Hello, I am trying to install Haploclique (on Ubuntu) and I always get the same error message:

CMake Warning at external/googletest/googletest/CMakeLists.txt:51 (project): VERSION keyword not followed by a value or was followed by a value that expanded to nothing.

Found Python: /usr/bin/python3.8 (found version "3.8.0") found components: Interpreter CMake Error at external/googletest/googletest/CMakeLists.txt:127 (set_target_properties): set_target_properties called with incorrect number of arguments.

CMake Error at external/googletest/googletest/CMakeLists.txt:129 (set_target_properties): set_target_properties called with incorrect number of arguments.

Configuring incomplete, errors occurred! See also "/home/natasa/Downloads/Programi/haploclique/build/CMakeFiles/CMakeOutput.log". See also "/home/natasa/Downloads/Programi/haploclique/build/CMakeFiles/CMakeError.log".

I would be really grateful if you could give me some advice, because I found this software perfect for my research and I would really like to find a way to use it.

Thank you so much in advance! Natasa

[DrYak]

Dear Natasa,

I haven't been recompiling Haploclique for quite some time, so I am not entirely aware of any subtlety that might have crept recently. (We switched to using SAVAGE in our V-pipe, and are considering PredictHaplo in the future for which we will be taking over the maintenance).

As a general note:

• Haploclique is also available on bioconda as a precompiled and ready-to-use package, if you just need to experiment the software, that's the easiest way (and that's how we do it in V-pipe and most other snakemake workflows).
• The recipe I wrote for bioconda might be source of clues (Did you install all the dependencies such as e.g. jsoncpp ?)
• The circleci test that Armin wrote might be another source of clues.

[natasacirovic]

Dear Ivan, Yes, I tried SAVAGE, but unfortunately almoust all my jobs on a cluster failed and I always get the same error message. That was the reason why I wanted to switch to HaploClique and try to reconstruct global haplotypes using it instead of SAVAGE. Maybe I do something wrong, but there are also couple of jobs which are compleated (including global hpl), and that makes me think that I didn’t make mistake in a config file or running a pipline. The other reason is that I assumed that HaploClique is faster (according to your V-pipe article). My jobs take around 4-5 weeks to finish (using 32 thereads) and at the end a lot of them fail when it comes to global haplotype reconstruction. If you have any advice, I would be very happy :) Best, Natasa