search

marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Other
126 stars 25 forks source link

-l libMUSCLE #57

Closed tseemann closed 4 years ago

tseemann commented 6 years ago

This fails on modern g++

g++-5 -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -lgomp 
-lstdc++ -lpthread -std=gnu++0x 
-Wl,-rpath,/tmp/parsnp-20180811-9069-15u0ftn/parsnp-1.2/muscle/lib 
-L/tmp/parsnp-20180811-9069-15u0ftn/parsnp-1.2/muscle/lib -lMUSCLE-3.7 
-o parsnp 
parsnp-MuscleInterface.o parsnp-parsnp.o parsnp-LCB.o parsnp-LCR.o 
parsnp-TMum.o parsnp-Converter.o parsnp-iniFile.o

because

-lMUSCLE-3.7 needs to come after the object files.

treangen commented 5 years ago

thanks Torsten, good catch

tseemann commented 5 years ago

It was @sjackman who figured it out for me :)

advaitb commented 4 years ago

Added the fix to build_parsnp_linux.sh. Should work now :)

tseemann commented 4 years ago

This is not a linux issue. it will still happen on MacOS if you use g++ compiler.