redndgreen8
commented
1 year ago https://github.com/ChaissonLab/hmcnc this is the most updated version in c++
Closed splaisan closed 1 year ago
redndgreen8
commented
1 year ago https://github.com/ChaissonLab/hmcnc this is the most updated version in c++
splaisan
commented
1 year ago 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.txtthere 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
Hi, I was pointed to this tool for PB HiFi data analysis
I built the env as instructed but when it comes to scipy=0.15.0 it is not found by conda (or mamba) Any idea what I can do to fix this? can I use the scipy version 1.7.3 proposed by mamba? (seems to work)
Also, is there a tutorial on how to use the commands? the dry command output is not very explicit on where to get the inputs!
Thanks