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redndgreen8 avatar redndgreen8 commented on May 25, 2024

https://github.com/ChaissonLab/hmcnc
this is the most updated version in c++

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splaisan avatar splaisan commented on May 25, 2024

HI @redndgreen8,
I am trying to build that version but it fails on me with dependencies which are not listed (and there is no issue page on that repo!)
Can you please share where I can find the missing cram program? (I installed samtools 1.18 and htslib but they do not seem to suffice)
Thanks

The Meson build system
Version: 0.53.2
Source dir: /opt/biotools/hmcnc
Build dir: /opt/biotools/hmcnc/build
Build type: native build
Project name: hmcnc
Project version: 0.0.1
C compiler for the host machine: cc (gcc 9.4.0 "cc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0")
C linker for the host machine: cc ld.bfd 2.34
C++ compiler for the host machine: c++ (gcc 9.4.0 "c++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0")
C++ linker for the host machine: c++ ld.bfd 2.34
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C++ supports arguments -Wduplicated-cond: YES 
Compiler for C++ supports arguments -Wduplicated-branches: YES 
Compiler for C++ supports arguments -Wlogical-op: YES 
Compiler for C++ supports arguments -Wrestrict: YES 
Compiler for C++ supports arguments -Wnull-dereference: YES 
Compiler for C++ supports arguments -Wuseless-cast: YES 
Compiler for C++ supports arguments -Wdouble-promotion: YES 
Compiler for C++ supports arguments -Wshadow: YES 
Compiler for C++ supports arguments -Wformat=1: YES 
Run-time dependency Boost found: YES 1.71
Run-time dependency threads found: YES
Found pkg-config: /usr/bin/pkg-config (0.29.1)
Run-time dependency htslib found: YES 1.15.1
Run-time dependency zlib found: YES 1.2.11
Run-time dependency GTest found: YES 1.10.0
Program cram found: NO

tests/cram/meson.build:5:0: ERROR: Program(s) ['cram'] not found or not executable

A full log can be found at /opt/biotools/hmcnc/build/meson-logs/meson-log.txt

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redndgreen8 avatar redndgreen8 commented on May 25, 2024

there is a makefile in src/ that you can also use, I would recommend using that with a conda env with all the listed programs and gxx

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