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harisankarsadasivan / RawMap

Complements Minimap2 for a fast and efficient Read-Until pipeline
MIT License
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locating hdf5.h #2

Open hasindu2008 opened 1 year ago

hasindu2008 commented 1 year ago

I am trying to compile RawMap and encountering this issue:

g++ -Wall -std=c++11 -O3 -DUSE_OPENCV_GRID_SEARCH_AUTOTRAIN -DMED_VAR RawMap.cpp -lz -lm -lstdc++ -ldl -lhdf5  -I/usr/include/opencv `pkg-config opencv --cflags --libs` -o RawMap
In file included from fast5/nanopolish_fast5_io.cpp:13:0,
                 from RawMap.cpp:11:
fast5/nanopolish_fast5_io.h:15:18: fatal error: hdf5.h: No such file or directory
compilation terminated.
Makefile:8: recipe for target 'RawMap' failed
make: *** [RawMap] Error 1

NOTE: I installed HDF5 using the provided install install_hdf5.sh script. Anything I am missing?

harisankarsadasivan commented 1 year ago

Excited to see your interest. Ah, seems to be a linker issue. I'll fix, test on a new machine and update here. I'll leave this open for now. Unfortunately, I'm quite packed for 2 weeks with my PhD thesis proposal and job interviews. Thank You.

hasindu2008 commented 1 year ago

No worries. I anyway spent like 15 mins and implemented BLOW5 support instead. https://github.com/harisankarsadasivan/RawMap/pull/3 and got that to compile and run. Not sure if the training results are as it should be.