def make_module_extra(self):
"""Add install path to PERL*LIB"""
majver = get_major_perl_version()
sitearchsuffix = get_sitearch_suffix()
# also add sitearch dir to Perl search path
txt = self.moduleGenerator.prepend_paths("PERL%sLIB" % majver,
['', sitearchsuffix])
return ExtensionEasyBlock.make_module_extra(self, txt)
def make_module_req_guess(self):
"""Customized dictionary of paths to look for with PERL*LIB."""
majver = get_major_perl_version()
sitearchsuffix = get_site_suffix("sitearch")
sitelibsuffix = get_site_suffix("sitelib")
guesses = super(PerlModule, self).make_module_req_guess()
guesses.update({"PERL%sLIB" % majver: ["", sitearchsuffix, sitelibsuffix]})
return guesses
def make_module_req_guess(self):
"""Custom guesses for environment variables (PATH, ...) for VEP."""
perl_majver = get_major_perl_version()
guesses = super(EB_VEP, self).make_module_req_guess()
guesses = {
'PATH': '',
'PERL%sLIB' % perl_majver: self.api_mods_subdir,
}
return guesses
def make_module_req_guess(self):
"""Custom guesses for environment variables (PATH, ...) for VEP."""
perl_majver = get_major_perl_version()
guesses = super(EB_VEP, self).make_module_req_guess()
guesses = {
'PATH': '',
'PERL%sLIB' % perl_majver: self.api_mods_subdir,
}
return guesses
def make_module_req_guess(self):
"""Customized dictionary of paths to look for with PERL*LIB."""
majver = get_major_perl_version()
sitearchsuffix = get_site_suffix('sitearch')
sitelibsuffix = get_site_suffix('sitelib')
guesses = super(PerlModule, self).make_module_req_guess()
guesses.update({
"PERL%sLIB" % majver: ['', sitearchsuffix, sitelibsuffix],
})
return guesses
def make_module_extra(self):
"""Correctly prepend $PATH and $PERLXLIB for MUMmer."""
# determine major version for Perl (e.g. '5'), required for e.g. $PERL5LIB
perlmajver = get_major_perl_version()
# set $PATH and $PERLXLIB correctly
txt = super(EB_MUMmer, self).make_module_extra()
txt += self.module_generator.prepend_paths("PATH", ['bin'])
txt += self.module_generator.prepend_paths("PATH", ['bin/aux_bin'])
txt += self.module_generator.prepend_paths("PERL%sLIB" % perlmajver, ['bin/scripts'])
return txt
def install_step(self):
"""Custom install procedure for VEP."""
# patch INSTALL.pl script to use https:// rather than ftp://
apply_regex_substitutions('INSTALL.pl', [('ftp://', 'https://')])
# update PERL5LIB so tests can run (done automatically by INSTALL.pl unless --NO_TEST is used)
perl_majver = get_major_perl_version()
perllib_envvar = 'PERL%sLIB' % perl_majver
perllib = os.getenv(perllib_envvar, '')
api_mods_dir = os.path.join(self.installdir, self.api_mods_subdir)
self.log.info("Adding %s to $%s (%s)", api_mods_dir, perllib_envvar,
perllib)
env.setvar(perllib_envvar, '%s:%s' % (api_mods_dir, perllib))
# check for bundled dependencies
bundled_deps = [
# tuple format: (package name in EB, option name for INSTALL.pl)
('BioPerl', 'NO_BIOPERL'),
('Bio-DB-HTS', 'NO_HTSLIB'),
]
installopt_deps = []
for (dep, opt) in bundled_deps:
if get_software_root(dep):
installopt_deps.append('--%s' % opt)
installopt_deps = ' '.join(installopt_deps)
# see https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer
cmd = ' '.join([
self.cfg['preinstallopts'],
'perl',
'INSTALL.pl',
# disable installation of bundled dependencies that are provided as dependencies in the easyconfig
installopt_deps,
# a: API, f: FASTA
# not included:
# c: cache, should be downloaded by user
# l: Bio::DB::HTS, should be provided via EasyBuild
# p: plugins
'--AUTO af',
# install all species
'--SPECIES all',
# don't update VEP during installation
'--NO_UPDATE',
# location to install Perl API modules into
'--DESTDIR ' + api_mods_dir,
self.cfg['installopts'],
])
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
def make_module_req_guess(self):
"""Custom guesses for environment variables (PATH, ...) for VEP."""
perl_majver = get_major_perl_version()
perl_libpath = [self.api_mods_subdir]
if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]:
perl_ver = get_software_version('Perl')
perl_libpath.extend([os.path.join('lib', 'perl' + perl_majver, 'site_perl', perl_ver)])
guesses = super(EB_VEP, self).make_module_req_guess()
guesses = {
'PATH': '',
'PERL%sLIB' % perl_majver: perl_libpath,
}
return guesses
def sanity_check_step(self):
"""Custom sanity check for VEP."""
custom_paths = {
'files': ['vep'],
'dirs': ['modules/Bio/EnsEMBL/VEP'],
}
if 'Bio::EnsEMBL::XS' in [ext[0] for ext in self.cfg['exts_list']]:
perl_majver = get_major_perl_version()
perl_ver = get_software_version('Perl')
perl_libpath = os.path.join('lib', 'perl' + perl_majver, 'site_perl', perl_ver)
bio_ensembl_xs_ext = os.path.join(perl_libpath, 'x86_64-linux-thread-multi', 'Bio', 'EnsEMBL', 'XS.pm')
custom_paths['files'].extend([bio_ensembl_xs_ext])
custom_commands = ['vep --help']
super(EB_VEP, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
def install_step(self):
"""Custom install procedure for VEP."""
# patch INSTALL.pl script to use https:// rather than ftp://
apply_regex_substitutions('INSTALL.pl', [('ftp://', 'https://')])
# update PERL5LIB so tests can run (done automatically by INSTALL.pl unless --NO_TEST is used)
perl_majver = get_major_perl_version()
perllib_envvar = 'PERL%sLIB' % perl_majver
perllib = os.getenv(perllib_envvar, '')
api_mods_dir = os.path.join(self.installdir, self.api_mods_subdir)
self.log.info("Adding %s to $%s (%s)", api_mods_dir, perllib_envvar,
perllib)
env.setvar(perllib_envvar, '%s:%s' % (api_mods_dir, perllib))
# see https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer
cmd = ' '.join([
self.cfg['preinstallopts'],
'perl',
'INSTALL.pl',
# don't try to install optional Bio::DB::HTS (can be provided as an extension instead)
'--NO_HTSLIB',
# a: API, f: FASTA
# not included:
# c: cache, should be downloaded by user
# l: Bio::DB::HTS, should be provided via EasyBuild
# p: plugins
'--AUTO af',
# install all species
'--SPECIES all',
# don't update VEP during installation
'--NO_UPDATE',
# location to install Perl API modules into
'--DESTDIR ' + api_mods_dir,
self.cfg['installopts'],
])
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
def install_step(self):
"""Custom install procedure for VEP."""
# patch INSTALL.pl script to use https:// rather than ftp://
apply_regex_substitutions('INSTALL.pl', [('ftp://', 'https://')])
# update PERL5LIB so tests can run (done automatically by INSTALL.pl unless --NO_TEST is used)
perl_majver = get_major_perl_version()
perllib_envvar = 'PERL%sLIB' % perl_majver
perllib = os.getenv(perllib_envvar, '')
api_mods_dir = os.path.join(self.installdir, self.api_mods_subdir)
self.log.info("Adding %s to $%s (%s)", api_mods_dir, perllib_envvar, perllib)
env.setvar(perllib_envvar, '%s:%s' % (api_mods_dir, perllib))
# see https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer
cmd = ' '.join([
self.cfg['preinstallopts'],
'perl',
'INSTALL.pl',
# don't try to install optional Bio::DB::HTS (can be provided as an extension instead)
'--NO_HTSLIB',
# a: API, f: FASTA
# not included:
# c: cache, should be downloaded by user
# l: Bio::DB::HTS, should be provided via EasyBuild
# p: plugins
'--AUTO af',
# install all species
'--SPECIES all',
# don't update VEP during installation
'--NO_UPDATE',
# location to install Perl API modules into
'--DESTDIR ' + api_mods_dir,
self.cfg['installopts'],
])
run_cmd(cmd, log_all=True, simple=True, log_ok=True)