Not compiling SuperReads_RNA

[rafaeltiveron]

I've tried to compile jellyfish and quorum. But it didn't work. So, I downloaded all packages from github specific directories and compiled everything. In the end, a error message for SuperRead compilation:

CXX      src/sorted_merge.o
  CXX      src/create_k_unitigs_large_k.o
  CXX      src/create_k_unitigs_large_k2.o
  CXX      src/bloom_query.o
  CXX      src/rename_filter_fastq.o
  CXX      src/read_parser.o
  CXX      src2/findMatchesBetweenKUnitigsAndReads.o
  CXX      src2/createKUnitigMaxOverlaps.o
mkdir -p src/
  CXX      src2/getSuperReadInsertCountsFromReadPlacementFile.o
  CXX      src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o
  CXX      src2/joinKUnitigs_v3.o
sed -e 's,[@]bindir[@],/usr/local/stringtie/test/stringtie-2.2.1/SuperReads_RNA/bin,g' \
    -e 's,[@]libdir[@],/usr/local/stringtie/test/stringtie-2.2.1/SuperReads_RNA/lib,g' \
    -e 's,[@]PERL_EXT_DIR[@],/usr/local/stringtie/test/stringtie-2.2.1/SuperReads_RNA/lib/perl,g' < src/MasurcaPaths.pm.in > src/MasurcaPaths.pm
chmod +x src/MasurcaPaths.pm
  CXXLD    rename_filter_fastq
  CXXLD    bloom_query
/usr/bin/ld: src/bloom_query.o: warning: relocation against `_ZN9jellyfish10mer_dna_ns18error_short_stringE' in read-only section `.text.unlikely
/usr/bin/ld: src/bloom_query.o: in function `jellyfish::mer_dna_ns::mer_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0> >::operatord::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
/usr/local/stringtie/test/stringtie-2.2.1/SuperReads_RNA/global-1/SuperReadsR/./jellyfish/mer_dna.hpp:312: undefined reference to `jellyfish::mer_ns::error_short_string'
/usr/bin/ld: warning: creating DT_TEXTREL in a PIE
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1166: bloom_query] Erro 1
make[2]: ** Esperando que outros processos terminem.
make[2]: Saindo do diretório '/usr/local/stringtie/test/stringtie-2.2.1/SuperReads_RNA/global-1/SuperReadsR'
make[1]: *** [Makefile:2111: install] Erro 2
make[1]: Saindo do diretório '/usr/local/stringtie/test/stringtie-2.2.1/SuperReads_RNA/global-1/SuperReadsR'
make: *** [Makefile:847: install-special] Erro 2

Some new versions gcc, python, etc... It should be a new stringtie version too!

[SchwarzEM]

I encountered similar problems with compiling SuperReads_RNA.

I solved them by not working with the very latest github code, but instead with the latest stable release of StringTie2. When I used that, everything including SuperReads_RNA compiled cleanly.

My line-commands were:

cd $PROJECT/src/unpack ;

wget https://github.com/gpertea/stringtie/archive/refs/tags/v2.2.1.tar.gz ;
zcat v2.2.1.tar.gz | tar xf - ;
mv -i stringtie-2.2.1 $PROJECT/src ;

cd $PROJECT/src/stringtie-2.2.1 ;
make release ;
./stringtie -h ;    # it was compiled, and it works

cd SuperReads_RNA ;
./install.sh ;
./create_rna_sr.py ;   # it was compiled, and it works!