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jfarek / xatlas

BSD 3-Clause "New" or "Revised" License
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Install issues #3

Closed colindaven closed 6 years ago

colindaven commented 6 years ago

It would ease installation to have an example of downloading a compatible HTSlib and pointing the configure at it.

I have tried multiple variants of the below and do not know what to expect or where it wants htslib/hts.h to be present. Linking ln -s does not work

cheers

./configure --enable-multithreading --with-htslib-lib=htslib-1.4.1 rcug@hpc03:/mnt/ngsnfs/tools/xatlas$ ./configure --enable-multithreading --with-htslib-lib=htslib-1.4.1 checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking htslib/hts.h usability... no checking htslib/hts.h presence... no checking for htslib/hts.h... no configure: error: Failed to find HTSLib headers

jfarek commented 6 years ago

Hi,

If the htslib header files subdirectory (htslib/) is also located in the same directory htslib-1.4.1, you can run configure as:

./configure --enable-multithreading --with-htslib=htslib-1.4.1

If htslib/ is located somewhere else, you can specify its location with the --with-htslib-include= option:

./configure --enable-multithreading --with-htslib-lib=htslib-1.4.1 --with-htslib-include=/path/to/htslib_dir

colindaven commented 6 years ago

Repeatedly tried with all sorts of new downloads, various htslib, compiled or non-compiled htslibs, no signs of progress, thanks anyway.

loreseeker commented 5 years ago

@colindaven Hi, I ran into the same issue, but was able to build alignstats-0.7 on a clean ubuntu:16.04 after adding a make install command for htslib-1.9 and to run it after exporting LD_LIBRARY_PATH to include htslib-1.9 directory