TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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Can't compile #168

Open theo-allnutt-bioinformatics opened 2 years ago

theo-allnutt-bioinformatics commented 2 years ago

Hi,

unfortunately I cannot use conda on the HPC I am using. When compiling I get the following error:

/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[4]: [Makefile:1156: bin/kat_jellyfish] Error 1 make[4]: Leaving directory '/g/data/nm31/bin/KAT/deps/jellyfish-2.2.0' make[3]: [Makefile:1867: all-recursive] Error 1 make[3]: Leaving directory '/g/data/nm31/bin/KAT/deps/jellyfish-2.2.0' make[2]: [Makefile:901: all] Error 2 make[2]: Leaving directory '/g/data/nm31/bin/KAT/deps/jellyfish-2.2.0' make[1]: [Makefile:475: all-recursive] Error 1 make[1]: Leaving directory '/g/data/nm31/bin/KAT' make: *** [Makefile:399: all] Error 2

tallnuttrbgv commented 2 years ago

Tried this:

edited build_boost.sh and replace '--prefix=build' with '--prefix=/g/data/nm31/bin/KAT' ./build_boost.sh

./autogen.sh

./configure --prefix=/g/data/nm31/bin/KAT

make

And get this error:

Making install in lib make[1]: Entering directory '/g/data/nm31/bin/KAT/lib' CXX src/libkat_la-matrix_metadata_extractor.lo In file included from src/matrix_metadata_extractor.cc:23: ../lib/include/kat/matrix_metadata_extractor.hpp:24:10: fatal error: boost/filesystem/path.hpp: No such file or directory 24 | #include <boost/filesystem/path.hpp> | ^~~~~~~ compilation terminated. make[1]: [Makefile:551: src/libkat_la-matrix_metadata_extractor.lo] Error 1 make[1]: Leaving directory '/g/data/nm31/bin/KAT/lib' make: [Makefile:475: install-recursive] Error 1