Install fails because of HDF5 file

[jayradke]

Installation fails. Can’t access the HDF5 site. Any plans to fix this again or is nanopolish not accessible to those that didn’t install 2 years ago?

[jts]

I just tried a clean install and it worked. Please provide some details (OS, build error log).

[jayradke]

Will get you that info after I try another clean install. Using Docker for install didn’t work either.

[jayradke]

where would i find the build error log?

[jayradke]

This is what is shown before the make quits

echo '# Default htscodecs.mk generated by Makefile' > htscodecs.mk gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c

gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c bgzf.c:38:10: fatal error: zlib.h: No such file or directory

include

      ^~~~~~~~

compilation terminated. make[1]: [Makefile:164: bgzf.o] Error 1 make[1]: Leaving directory '/home/jayradke/nanopolish/htslib' make: [Makefile:139: htslib/libhts.a] Error 255

[jts]

That's not an HDF5 error. See here: https://github.com/jts/nanopolish/issues/125

[jayradke]

when i do the sudo apt-get install zlib1g-dev it says....

zlib1g-dev is already the newest version (1:1.2.11.dfsg-2ubuntu9.2). 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.

if i run make after that..

make[1]: Entering directory '/home/jayradke/nanopolish_010824/htslib' gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c bgzf.c:38:10: fatal error: zlib.h: No such file or directory

include

      ^~~~~~~~

compilation terminated. make[1]: [Makefile:164: bgzf.o] Error 1 make[1]: Leaving directory '/home/jayradke/nanopolish_010824/htslib' make: [Makefile:139: htslib/libhts.a] Error 255

not sure what i did wrong with the zlib1g-dev step

[jayradke]

tried was was recommend in #125. event and down loaded zlib_1.3 and went through the process to install zlib from here https://www.linuxcapable.com/how-to-install-zlib-on-ubuntu-linux/ Still cant find zlib.h. is this because I am using WSL2 Ubuntu-22.04?

i can find the zlib.h and zconf.h in my usr/local/zlib/include

[jayradke]

so i copy and pasted those two files into htslib and got past that error to this

/home/jayradke/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz /home/jayradke/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lbz2 collect2: error: ld returned 1 exit status make[1]: [Makefile:316: libhts.so] Error 1 make[1]: Leaving directory '/home/jayradke/nanopolish/htslib' make: [Makefile:139: htslib/libhts.a] Error 255

[jts]

both the header files (zlib.h) and the compiled libraries are needed to compile htslib/nanopolish. I don't use WSL2 so it is hard to say why they can't be found. On standard ubuntu systems running sudo apt-get install zlib1g-dev should be sufficient. I suspect an environment variable isn't being set.