make VEP easyblock compatible with --sanity-check-only

[boegel]

Without this fix, perl_ver is defined as None in sanity_check_step when using --sanity-check-only, because the module is not loaded yet when get_software_root('Perl') is being called.

During an actual build the dependencies are loaded already/still via prepare_step at that point...

Fixes this crash when using --sanity-check-only:

$ eb VEP-105-GCC-11.2.0.eb --sanity-check-only
...

ERROR: Traceback (most recent call last):
  File "/home/example/easybuild/easybuild-framework/easybuild/main.py", line 128, in build_and_install_software
    (ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
  File "/home/example/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 4058, in build_and_install_one
    result = app.run_all_steps(run_test_cases=run_test_cases)
  File "/home/example/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3941, in run_all_steps
    self.run_step(step_name, step_methods)
  File "/home/example/easybuild/easybuild-framework/easybuild/framework/easyblock.py", line 3776, in run_step
    step_method(self)()
  File "/home/example/easybuild/easybuild-easyblocks/easybuild/easyblocks/v/vep.py", line 120, in sanity_check_step
    perl_libpath = os.path.join('lib', 'perl' + perl_majver, 'site_perl', perl_ver)
  File "/usr/lib64/python3.6/posixpath.py", line 94, in join
    genericpath._check_arg_types('join', a, *p)
  File "/usr/lib64/python3.6/genericpath.py", line 149, in _check_arg_types
    (funcname, s.__class__.__name__)) from None
TypeError: join() argument must be str or bytes, not 'NoneType'

[ocaisa]

Test report by @ocaisa

Overview of tested easyconfigs (in order)

• FAIL (build issue) VEP-103.1-GCC-10.2.0.eb (partial log available at https://gist.github.com/dca6afe1f545d7f2b20305ebb4140ff3)
• FAIL (build issue) VEP-105-GCC-11.2.0.eb (partial log available at https://gist.github.com/467851c59e9a7b2b5fb0ce95d73f7663)

Build succeeded for 0 out of 2 (2 easyconfigs in total)
login1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz, Python 3.6.8
See https://gist.github.com/566da4139a5ada0eb16df36d5cc169f6 for a full test report.

[ocaisa]

@boegel sanity is failing even though the files are actually there:

== sanity checking...
  >> file 'vep' found: FAILED
  >> file 'lib/perl5/site_perl/5.34.0/x86_64-linux-thread-multi/Bio/EnsEMBL/XS.pm' found: FAILED
  >> (non-empty) directory 'modules/Bio/EnsEMBL/VEP' found: FAILED

[ocaisa]

Test report by @ocaisa

Overview of tested easyconfigs (in order)

• SUCCESS VEP-103.1-GCC-10.2.0.eb
• SUCCESS VEP-105-GCC-11.2.0.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
login1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz, Python 3.6.8
See https://gist.github.com/088f098fe114456486e7a4200fa66bf3 for a full test report.

[ocaisa]

Ah, I had the "wrong" install path set. Hmm, this is actually in weakness in --sanity-check-only, it should be using the module to decide what the root path is for the installation.

[boegel]

Ah, I had the "wrong" install path set. Hmm, this is actually in weakness in --sanity-check-only, it should be using the module to decide what the root path is for the installation.

Hmm, good point. Please open a framework issue on that...