update VEP easyblock to make installation compatible with Bio::EnsEMBL::XS #1828
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houndci-bot
reviewed
Oct 14, 2019
easybuild/easyblocks/v/vep.py
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| if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]: | ||
| custom_paths['files'] += ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/EnsEMBL/XS.pm'\ | ||
| % (get_major_perl_version(), get_software_version('Perl'))] |
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continuation line under-indented for visual indent
easybuild/easyblocks/v/vep.py
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| custom_paths = { | ||
| 'files': ['vep'], | ||
| 'dirs': ['modules/Bio/EnsEMBL/VEP'], | ||
| } | ||
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| if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]: | ||
| custom_paths['files'] += ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/EnsEMBL/XS.pm'\ |
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the backslash is redundant between brackets
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@lexming Please use extend, use os.path.join and avoid breaking the long line by using a local variable:
if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]:
perl_maj_ver = get_major_perl_version()
perl_ver = get_software_version('Perl')
perl_lib_subdir = os.path.join('lib', 'perl' + perl_maj_ver, 'site_perl', perl_ver)
bio_ensembl_xs_perl_mod = os.path.join(perl_lib_subdir, 'x86_64-linux-thread-multi', Bio', 'EnsEMBL', 'XS.pm')
custom_paths['files'].extend(bio_ensembl_xs_perl_mod)There was a problem hiding this comment.
Fixed with your suggestions. Thanks for the feedback.
boegel
requested changes
Oct 14, 2019
easybuild/easyblocks/v/vep.py
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| custom_paths = { | ||
| 'files': ['vep'], | ||
| 'dirs': ['modules/Bio/EnsEMBL/VEP'], | ||
| } | ||
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| if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]: | ||
| custom_paths['files'] += ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Bio/EnsEMBL/XS.pm'\ |
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@lexming Please use extend, use os.path.join and avoid breaking the long line by using a local variable:
if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]:
perl_maj_ver = get_major_perl_version()
perl_ver = get_software_version('Perl')
perl_lib_subdir = os.path.join('lib', 'perl' + perl_maj_ver, 'site_perl', perl_ver)
bio_ensembl_xs_perl_mod = os.path.join(perl_lib_subdir, 'x86_64-linux-thread-multi', Bio', 'EnsEMBL', 'XS.pm')
custom_paths['files'].extend(bio_ensembl_xs_perl_mod)
easybuild/easyblocks/v/vep.py
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| @@ -105,9 +112,13 @@ def make_module_req_guess(self): | |||
| """Custom guesses for environment variables (PATH, ...) for VEP.""" | |||
| perl_majver = get_major_perl_version() | |||
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| perl_libpath = [self.api_mods_subdir] | |||
| if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]: | |||
| perl_libpath += ['lib/perl%s/site_perl/%s' % (perl_majver, get_software_version('Perl'))] | |||
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same here, please use .extend and os.path.join
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perl_maj_ver = get_major_perl_version()
perl_ver = get_software_version('Perl')
perl_libpath.extend(os.path.join('lib', 'perl' + perl_maj_ver, 'site_perl', perl_ver)
boegel
changed the title
boegel
approved these changes
Oct 14, 2019
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tested with existing Thanks @lexming! |
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Update for
vepeasyblock to add sanity checks and set specific environment variables for the extensionBio::EnsEMBL::XSif it is present in the list of extension list.