Have been struggling to set up my environment to run bioinformatics tools. The issue started with a consistent autogen.sh error in autoreconf -fi: command not found for multiple applications. Reinstalled autoconf, automake, libtools.
Currently, libtools installation fails at ./configure, but autoconf and automake installed successfully.
Here is the error:
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... libltdl/config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-apple-darwin18.0.0
checking host system type... x86_64-apple-darwin18.0.0
configure: autobuild project... GNU Libtool
configure: autobuild revision... 2.4.2 ()
configure: autobuild hostname... MACUSR
configure: autobuild mode... default
configure: autobuild timestamp... 2019011
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... configure: error: in `/usr/local/libtool-2.4.2':
configure: error: cannot run C compiled programs.
Tried Homebrew, it installed all my tools in usr/local/Cellar and nothing runs, I have added tool locations to my PATH variable, but no luck. Traced problem to jamf issue: https://www.jamf.com/jamf-nation/discussions/28764/jamf-quickadd-symlinks-usr-local-bin-causing-install-problems-for-other-apps
Stuck and will be happy for an advice here.