Error while installing Minia on Linux

Question

[Ashi]

I have been trying to install the short read assembler Minia on my linux system but whenever I am giving the "make" command this error is coming up.

[ 71%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o
In file included from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:35,
             from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:33,
             from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509,
             from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666,
             from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:43,
             from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20,
             from /home/minia/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5
 /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp: In copy constructor 
'gatb::core::tools::collections::impl::IteratorGzFile<Item>::IteratorGzFile(const 
gatb::core::tools::collections::impl::IteratorGzFile<Item>&)':
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:242:9: error: there are no 
arguments to 'gzbuffer' that depend on a template parameter, so a declaration of 'gzbuffer' must be available [- 
fpermissive]
242 |         gzbuffer(_gzfile,2*1024*1024);
  |         ^~~~~~~~
   /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:242:9: note: (if you use '- 
fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp: In constructor 
'gatb::core::tools::collections::impl::IteratorGzFile<Item>::IteratorGzFile(const string&, size_t)':
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:252:9: error: there are no 
 arguments to 'gzbuffer' that depend on a template parameter, so a declaration of 'gzbuffer' must be available [- 
 fpermissive]
  252 |         gzbuffer(_gzfile,2*1024*1024);
   |         ^~~~~~~~
  /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp: In member function 
 'gatb::core::tools::collections::impl::IteratorGzFile<Item>& 
 gatb::core::tools::collections::impl::IteratorGzFile<Item>::operator=(const 
 gatb::core::tools::collections::impl::IteratorGzFile<Item>&)':
 /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:278:13: error: there are 
 no arguments to 'gzbuffer' that depend on a template parameter, so a declaration of 'gzbuffer' must be available [- 
fpermissive]
 278 |             gzbuffer(_gzfile,2*1024*1024);
  |             ^~~~~~~~
 make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore- 
 static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o] Error 1
 make[1]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2
 make: *** [all] Error 2

I am following the installation from their manual. Please can anyone help me? Thanks

[MSRS]

Miniconda can be used for minia installation.

conda install -c bioconda minia

[Asaf]

Or even better, use the corresponding biocontainers docker container and use it with docker/singularity

[Ashi]

@MSRS thank you so much.