Problem with installing CNVnator

Question

[Ivan]

In order to install and use CNVnator, I first had to get ROOT and modify my environmental variables. I checked that root is installed correctly by calling root - I had no problems here.

Then I downloaded CNVnator via git clone and did necessary steps - including ln -s "path-to-my-samtools" samtools which linked the samtools binaries and has the htslib subdirectory. However, there is no libhts.a file in htslib subdirectory. I did both make and make OMP=no in CNVnator directory, and had the following error both times:

g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\"  -I/home/ipokrova/app_folder/root/root/include      -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c cnvnator.cpp -o obj/cnvnator.o
In file included from cnvnator.cpp:14:0:
AliParser.hh:18:3: error: ‘samfile_t’ does not name a type
   samfile_t   *file;
   ^
AliParser.hh:19:3: error: ‘bam_index_t’ does not name a type
   bam_index_t *index;
   ^
AliParser.hh: In member function ‘std::string AliParser::getQueryName()’:
AliParser.hh:98:69: error: ‘bam1_qname’ was not declared in this scope
   inline string getQueryName() { return (record) ? bam1_qname(record) : ""; }
                                                                     ^
make: *** [obj/cnvnator.o] Error 1

How do I fix the problem and use CNVnator?

EDIT1 : Tried using conda

Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.                           failed                                                                          /

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - cnvnator -> python[version='>=3.9,<3.10.0a0']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package __glibc conflicts for:
python=3.7 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
cnvnator -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Running python --version I got the output of Python 3.8.1

[Pierre Lindenbaum]

use conda: https://anaconda.org/bioconda/cnvnator

[Ivan]

Tried that, and failed, I've edited the OP

Answer 1

[Ivan]

Per the abyzovlab gitHub post:

The issue is with CNVnator no longer supporting new ROOT releases, and samtools removing legacy samtools API . The creator recommends switching to CNVpytor.