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gymreklab / GangSTR

A tool for profiling long STRs from short reads
GNU General Public License v2.0
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Can't get past htslib update step when trying to build GangSTR #124

Closed jsquaredosquared closed 11 months ago

jsquaredosquared commented 11 months ago

Like the title says, I am unable to build GangSTR-2.5.0 successfully from either the tarball or source. I am attempting to do so in WSL (Ubuntu 22.04.3 LTS) in Windows 11.

[ 29%] Performing download step (git clone) for 'htslib'
-- htslib download command succeeded.  See also [...]/GangSTR-2.5.0-Source/build/thirdparty/htslib/src/htslib-stamp/htslib-download-*.log
[ 31%] Performing update step for 'htslib'
configure.ac: error: required file 'config.sub' not found
configure.ac: error: required file 'config.guess' not found
configure.ac:   try running autoreconf --install
make[2]: *** [CMakeFiles/htslib.dir/build.make:124: thirdparty/htslib/src/htslib-stamp/htslib-update] Error 1
make[1]: *** [CMakeFiles/Makefile2:160: CMakeFiles/htslib.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

After this step I have tried going to the htslib directory, typing autoreconf --install and then using the command ./configure --host=x86_64-pc-linux-gnu as per Bing AI's suggestion. However, it still fails with the following error:

[ 31%] Performing configure step for 'htslib'
checking for gcc... gcc
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... Invalid configuration `unknown-Linux': machine `unknown' not recognized
configure: error: /bin/bash ./config.sub unknown-Linux failed
make[2]: *** [CMakeFiles/htslib.dir/build.make:92: thirdparty/htslib/src/htslib-stamp/htslib-configure] Error 1
make[1]: *** [CMakeFiles/Makefile2:160: CMakeFiles/htslib.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

What can I do to fix this and build GangSTR successfully?

jsquaredosquared commented 11 months ago

I gave up and decided to use conda.