We wanted to try the biopieces tools, which require certain dependencies, such as ruby and perl, a.o. After running the installers, and consequently installing some ruby gems, we were not able to run our regular linux 'make' command anymore:
~$ make /var/lib/gems/1.9.1/gems/make-0.3.1/bin/make:1:in `top (required)>': uninitialized constant ELF (NameError) from /usr/local/bin/make:23:in `load' from /usr/local/bin/make:23:in `<main>'
If we specify the root directory /usr/bin/make, it does work.
For now, we are not using biopieces and we could uninstall everything. Is it possible to fix this, to get back where we were before?