Compiling error (fatal error: png.h: No such file or directory)

[GuangliangGao]

Can not find the file, png.h

pngwrite.c:7:10: fatal error: png.h: No such file or directory 7 | #include "png.h" // MUST come before common.h, due to setjmp checking in pngconf.h | ^~~ compilation terminated. make[1]: [../inc/common.mk:420: pngwrite.o] Error 1 make[1]: Leaving directory '/public_data/softwares/GenomeAlignmentTools/kent/src/lib' make: [makefile:9: topLibs] Error 2

[GuangliangGao]

Can not find the png.h file in the path :/public_data/softwares/GenomeAlignmentTools/

find /public_data/softwares/ -name png.h

/public_data/softwares/anaconda2/pkgs/libpng-1.6.32-hda9c8bc_2/include/libpng16/png.h /public_data/softwares/anaconda2/pkgs/libpng-1.6.32-hda9c8bc_2/include/png.h /public_data/softwares/anaconda2/pkgs/libpng-1.6.36-hbc83047_0/include/libpng16/png.h /public_data/softwares/anaconda2/pkgs/libpng-1.6.36-hbc83047_0/include/png.h /public_data/softwares/anaconda2/include/libpng16/png.h /public_data/softwares/anaconda2/include/png.h /public_data/softwares/anaconda3/pkgs/libpng-1.6.37-hbc83047_0/include/png.h /public_data/softwares/anaconda3/pkgs/libpng-1.6.37-hbc83047_0/include/libpng16/png.h /public_data/softwares/anaconda3/include/png.h /public_data/softwares/anaconda3/include/libpng16/png.h

[MichaelHiller]

Pls install libpng which should install png.h globally.

[GuangliangGao]

Thanks for your help. We also encounter another issue: /root/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/11.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: /root/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/11.2.0/../../../../lib/libcrypto.so: undefined reference to `clock_gettime@GLIBC_2.17' collect2: error: ld returned 1 exit status make[2]: [../../../inc/userApp.mk:31: ../../../../bin//axtChain] Error 1 make[2]: Leaving directory '/public_data/softwares/GenomeAlignmentTools/kent/src/hg/mouseStuff/axtChain' make[1]: [makefile:49: axtChain.all] Error 2 make[1]: Leaving directory '/public_data/softwares/GenomeAlignmentTools/kent/src/hg/mouseStuff' make: *** [makefile:22: userApps] Error 2

[MichaelHiller]

Looks like your system lacks a few kind-of-standard libs. Pls install libcrypto. You will likely also need libssl and libpthread.

2) If you want to compute alignment chains, using chainCleaner and RepeatFiller, pls give https://github.com/hillerlab/make_lastz_chains a try, which provides a full container and a nextflow pipeline for all these steps. We are still beta-test this and will move it inside TOGA at some point, but maybe this is more helpful for you