text: user1075: I am trying to use Ragout: https://github.com/fenderglass/Ragout
  to fill the gaps in my de novo genome assembly. You can access the article freely here: https://www.ncbi.nlm.nih.gov/pubmed/24931998
  For this, I first need to install Sibelia.
  I tried doing so by cloning the GitHub repository into output/software/ragout/ and then running the following command:
  git clone https://github.com/fenderglass/Ragout output/software/ragout
  
  python2 output/software/ragout/scripts/install-sibelia.py
  
  Installing Sibelia
  Downloading source...
  -- The CXX compiler identification is AppleClang 9.0.0.9000037
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- The C compiler identification is AppleClang 9.0.0.9000037
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Performing Test HAVE_UNKNOWN_WALL
  -- Performing Test HAVE_UNKNOWN_WALL - Success
  -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER
  -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER - Success
  -- Looking for inttypes.h
  -- Looking for inttypes.h - found
  -- Looking for memory.h
  -- Looking for memory.h - found
  -- Looking for stddef.h
  -- Looking for stddef.h - found
  -- Looking for stdint.h
  -- Looking for stdint.h - found
  -- Looking for stdlib.h
  -- Looking for stdlib.h - found
  -- Looking for string.h
  -- Looking for string.h - found
  -- Looking for strings.h
  -- Looking for strings.h - found
  -- Looking for sys/types.h
  -- Looking for sys/types.h - found
  -- Performing Test HAVE_INLINE
  -- Performing Test HAVE_INLINE - Success
  -- Performing Test HAVE___INLINE
  -- Performing Test HAVE___INLINE - Success
  -- Performing Test HAVE___INLINE__
  -- Performing Test HAVE___INLINE__ - Success
  -- Performing Test HAVE___DECLSPEC_DLLEXPORT_
  -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed
  -- Performing Test HAVE___DECLSPEC_DLLIMPORT_
  -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed
  -- Check size of uint8_t
  -- Check size of uint8_t - done
  -- Check size of int32_t
  -- Check size of int32_t - done
  -- Looking for PRId32
  -- Looking for PRId32 - found
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/build
  Scanning dependencies of target divsufsort
  [  4%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/divsufsort.o
  [  8%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/sssort.o
  [ 12%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/trsort.o
  [ 16%] Building C object libdivsufsort-2.0.1/lib/CMakeFiles/divsufsort.dir/utils.o
  [ 20%] Linking C static library libdivsufsort.a
  [ 20%] Built target divsufsort
  Scanning dependencies of target Sibelia
  [ 24%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:43:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence.h:103:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
        guard here, followed by #define of a different macro [-Wheader-guard]
  #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:39:9: note: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
        mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:120:27: warning: 
        'sem_init' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_init(hSemaphore, 0, init));
                            ^
  /usr/include/sys/semaphore.h:55:42: note: 'sem_init' has been explicitly marked
        deprecated here
  int sem_init(sem_t *, int, unsigned int) __deprecated;
                                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:124:27: warning: 
        'sem_destroy' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_destroy(hSemaphore));
                            ^
  /usr/include/sys/semaphore.h:53:26: note: 'sem_destroy' has been explicitly
        marked deprecated here
  int sem_destroy(sem_t *) __deprecated;
                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  3 warnings generated.
  [ 28%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:43:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence.h:103:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
        guard here, followed by #define of a different macro [-Wheader-guard]
  #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:39:9: note: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
        mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:120:27: warning: 
        'sem_init' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_init(hSemaphore, 0, init));
                            ^
  /usr/include/sys/semaphore.h:55:42: note: 'sem_init' has been explicitly marked
        deprecated here
  int sem_init(sem_t *, int, unsigned int) __deprecated;
                                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:44:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score.h:48:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:124:27: warning: 
        'sem_destroy' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_destroy(hSemaphore));
                            ^
  /usr/include/sys/semaphore.h:53:26: note: 'sem_destroy' has been explicitly
        marked deprecated here
  int sem_destroy(sem_t *) __deprecated;
                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  3 warnings generated.
  [ 32%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o
  [ 36%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o
  [ 40%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o
  [ 44%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o
  [ 48%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o
  [ 52%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o
  [ 56%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o
  [ 60%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o
  [ 64%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o
  [ 68%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o
  [ 72%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o
  [ 76%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o
  [ 80%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o
  [ 84%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o
  [ 88%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o
  [ 92%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o
  [ 96%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o
  [100%] Linking CXX executable Sibelia
  [100%] Built target Sibelia
  [ 20%] Built target divsufsort
  [100%] Built target Sibelia
  Install the project...
  -- Install configuration: "Release"
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/bin/Sibelia
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/NEWS.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/ANNOTATION.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/README.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/USAGE.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/INSTALL.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/SIBELIA.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/C-SIBELIA.md
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/LICENSE.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.segdup.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/genomes_permutations.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta
  Traceback (most recent call last):
    File "output/software/ragout/scripts/install-sibelia.py", line 111, in <module>
      sys.exit(main())
    File "output/software/ragout/scripts/install-sibelia.py", line 107, in main
      return int(not install_deps(args.prefix))
    File "output/software/ragout/scripts/install-sibelia.py", line 31, in install_deps
      return install_sibelia(prefix)
    File "output/software/ragout/scripts/install-sibelia.py", line 64, in install_sibelia
      shutil.copy(sibelia_bin_src, sibelia_bin_dst)
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 119, in copy
      copyfile(src, dst)
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile
      with open(dst, 'wb') as fdst:
  IOError: [Errno 2] No such file or directory: '/Users/cr517/Documents/phd/project/lib/Sibelia'
  
  As you can see, I get a lot of errors. Could someone help me, please?
  I also tried to install Sibelia following their instructions here: https://github.com/bioinf/Sibelia
  cd Sibelia/build
  ➜  build git:(master) cmake ../src
  -- The CXX compiler identification is AppleClang 9.0.0.9000037
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- The C compiler identification is AppleClang 9.0.0.9000037
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Performing Test HAVE_UNKNOWN_WALL
  -- Performing Test HAVE_UNKNOWN_WALL - Success
  -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER
  -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER - Success
  -- Looking for inttypes.h
  -- Looking for inttypes.h - found
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  -- Configuring done
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  ➜  build git:(master) make
  Scanning dependencies of target lagan
  [  3%] Creating directories for 'lagan'
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  rightinfluence.cpp:21:2: error: reference to 'end' is ambiguous
          end.score = -2;
          ^
  rightinfluence.cpp:3:18: note: candidate found by name lookup is 'end'
  Fragment origin, end;
                   ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1768:1: note: 
        candidate found by name lookup is 'std::__1::end'
  end(const _Cp& __c)
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1611:1: note: 
        candidate found by name lookup is 'std::__1::end'
  end(_Tp (&__array)[_Np])
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1760:1: note: 
        candidate found by name lookup is 'std::__1::end'
  end(_Cp& __c)
  ^
  rightinfluence.cpp:22:22: error: reference to 'end' is ambiguous
          origin.totalScore = end.totalScore = 0;
                              ^
  rightinfluence.cpp:3:18: note: candidate found by name lookup is 'end'
  Fragment origin, end;
                   ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1768:1: note: 
  
  ...
  
  user581: There is a link to compiled binaries for OSX on the project homepage
  
original_text: 1075: <p>I am trying to use Ragout: <a href="https://github.com/fenderglass/Ragout" rel="nofollow noreferrer">https://github.com/fenderglass/Ragout</a></p>
  
  <p>to fill the gaps in my <em>de novo</em> genome assembly. You can access the article freely here: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24931998" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/24931998</a></p>
  
  <p>For this, I first need to install Sibelia.</p>
  
  <p>I tried doing so by cloning the GitHub repository into output/software/ragout/ and then running the following command:</p>
  
  <pre><code>git clone https://github.com/fenderglass/Ragout output/software/ragout
  
  python2 output/software/ragout/scripts/install-sibelia.py
  
  Installing Sibelia
  Downloading source...
  -- The CXX compiler identification is AppleClang 9.0.0.9000037
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
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  -- The C compiler identification is AppleClang 9.0.0.9000037
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
  -- Detecting C compiler ABI info
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  -- Detecting C compile features
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  -- Performing Test HAVE_UNKNOWN_WALL
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  -- Performing Test HAVE_INLINE
  -- Performing Test HAVE_INLINE - Success
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  -- Performing Test HAVE___INLINE__ - Success
  -- Performing Test HAVE___DECLSPEC_DLLEXPORT_
  -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed
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  -- Looking for PRId32
  -- Looking for PRId32 - found
  -- Configuring done
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  -- Build files have been written to: /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/build
  Scanning dependencies of target divsufsort
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  [ 20%] Built target divsufsort
  Scanning dependencies of target Sibelia
  [ 24%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/align.h:43:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence.h:103:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
        guard here, followed by #define of a different macro [-Wheader-guard]
  #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:39:9: note: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
        mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
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  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:120:27: warning: 
        'sem_init' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_init(hSemaphore, 0, init));
                            ^
  /usr/include/sys/semaphore.h:55:42: note: 'sem_init' has been explicitly marked
        deprecated here
  int sem_init(sem_t *, int, unsigned int) __deprecated;
                                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/sibelia.cpp:8:
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  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:124:27: warning: 
        'sem_destroy' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_destroy(hSemaphore));
                            ^
  /usr/include/sys/semaphore.h:53:26: note: 'sem_destroy' has been explicitly
        marked deprecated here
  int sem_destroy(sem_t *) __deprecated;
                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  3 warnings generated.
  [ 28%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9:
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  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence.h:103:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
        guard here, followed by #define of a different macro [-Wheader-guard]
  #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/sequence/string_set_dependent_generous.h:39:9: note: 
        'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
        mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
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  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:120:27: warning: 
        'sem_init' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_init(hSemaphore, 0, init));
                            ^
  /usr/include/sys/semaphore.h:55:42: note: 'sem_init' has been explicitly marked
        deprecated here
  int sem_init(sem_t *, int, unsigned int) __deprecated;
                                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.cpp:9:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/postprocessor.h:10:
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  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/score/score_matrix.h:40:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/file.h:70:
  In file included from /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system.h:82:
  /Users/cr517/Documents/phd/project/sibelia-build/Sibelia-master/src/include/seqan/system/system_sema.h:124:27: warning: 
        'sem_destroy' is deprecated [-Wdeprecated-declarations]
              SEQAN_DO_SYS(!sem_destroy(hSemaphore));
                            ^
  /usr/include/sys/semaphore.h:53:26: note: 'sem_destroy' has been explicitly
        marked deprecated here
  int sem_destroy(sem_t *) __deprecated;
                           ^
  /usr/include/sys/cdefs.h:176:37: note: expanded from macro '__deprecated'
  #define __deprecated    __attribute__((deprecated))
                                         ^
  3 warnings generated.
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  Install the project...
  -- Install configuration: "Release"
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/bin/Sibelia
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/NEWS.md
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  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt
  -- Installing: /Users/cr517/Documents/phd/project/sibelia-build/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta
  Traceback (most recent call last):
    File "output/software/ragout/scripts/install-sibelia.py", line 111, in &lt;module&gt;
      sys.exit(main())
    File "output/software/ragout/scripts/install-sibelia.py", line 107, in main
      return int(not install_deps(args.prefix))
    File "output/software/ragout/scripts/install-sibelia.py", line 31, in install_deps
      return install_sibelia(prefix)
    File "output/software/ragout/scripts/install-sibelia.py", line 64, in install_sibelia
      shutil.copy(sibelia_bin_src, sibelia_bin_dst)
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 119, in copy
      copyfile(src, dst)
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile
      with open(dst, 'wb') as fdst:
  IOError: [Errno 2] No such file or directory: '/Users/cr517/Documents/phd/project/lib/Sibelia'
  </code></pre>
  
  <p>As you can see, I get a lot of errors. Could someone help me, please?</p>
  
  <p>I also tried to install Sibelia following their instructions here: <a href="https://github.com/bioinf/Sibelia" rel="nofollow noreferrer">https://github.com/bioinf/Sibelia</a></p>
  
  <pre><code>cd Sibelia/build
  ➜  build git:(master) cmake ../src
  -- The CXX compiler identification is AppleClang 9.0.0.9000037
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- The C compiler identification is AppleClang 9.0.0.9000037
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
  -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Performing Test HAVE_UNKNOWN_WALL
  -- Performing Test HAVE_UNKNOWN_WALL - Success
  -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER
  -- Performing Test HAVE_UNKNOWN_FOMIT_FRAME_POINTER - Success
  -- Looking for inttypes.h
  -- Looking for inttypes.h - found
  -- Looking for memory.h
  -- Looking for memory.h - found
  -- Looking for stddef.h
  -- Looking for stddef.h - found
  -- Looking for stdint.h
  -- Looking for stdint.h - found
  -- Looking for stdlib.h
  -- Looking for stdlib.h - found
  -- Looking for string.h
  -- Looking for string.h - found
  -- Looking for strings.h
  -- Looking for strings.h - found
  -- Looking for sys/types.h
  -- Looking for sys/types.h - found
  -- Performing Test HAVE_INLINE
  -- Performing Test HAVE_INLINE - Success
  -- Performing Test HAVE___INLINE
  -- Performing Test HAVE___INLINE - Success
  -- Performing Test HAVE___INLINE__
  -- Performing Test HAVE___INLINE__ - Success
  -- Performing Test HAVE___DECLSPEC_DLLEXPORT_
  -- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed
  -- Performing Test HAVE___DECLSPEC_DLLIMPORT_
  -- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed
  -- Check size of uint8_t
  -- Check size of uint8_t - done
  -- Check size of int32_t
  -- Check size of int32_t - done
  -- Looking for PRId32
  -- Looking for PRId32 - found
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /Users/cr517/Documents/phd/project/Sibelia/build
  ➜  build git:(master) make
  Scanning dependencies of target lagan
  [  3%] Creating directories for 'lagan'
  [  6%] Performing download step (DIR copy) for 'lagan'
  [  9%] No patch step for 'lagan'
  [ 12%] No update step for 'lagan'
  [ 15%] No configure step for 'lagan'
  [ 18%] Performing build step for 'lagan'
  rightinfluence.cpp:21:2: error: reference to 'end' is ambiguous
          end.score = -2;
          ^
  rightinfluence.cpp:3:18: note: candidate found by name lookup is 'end'
  Fragment origin, end;
                   ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1768:1: note: 
        candidate found by name lookup is 'std::__1::end'
  end(const _Cp&amp; __c)
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1611:1: note: 
        candidate found by name lookup is 'std::__1::end'
  end(_Tp (&amp;__array)[_Np])
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1760:1: note: 
        candidate found by name lookup is 'std::__1::end'
  end(_Cp&amp; __c)
  ^
  rightinfluence.cpp:22:22: error: reference to 'end' is ambiguous
          origin.totalScore = end.totalScore = 0;
                              ^
  rightinfluence.cpp:3:18: note: candidate found by name lookup is 'end'
  Fragment origin, end;
                   ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1768:1: note: 
  </code></pre>
  
  <p>...</p>
   581: <p>There is a link to compiled binaries for OSX on the <a href="http://bioinf.spbau.ru/sibelia" rel="nofollow noreferrer">project homepage</a></p>
  