#NEWLINE# def _install_brew_baseline( env , brew_cmd , ipkgs , packages ) : #NEWLINE# #INDENT# 'Install baseline brew components not handled by dependency system.\n\n    - Installation of required Perl libraries.\n    - Upgrades any package dependencies\n    ' #NEWLINE# for dep in [ 'openssl' ] : #NEWLINE# #INDENT# _safe_link_pkg ( env , dep , brew_cmd ) #NEWLINE# #UNINDENT# for dep in [ 'expat' , 'pkg-config' , 'xz' , 'unzip' ] : #NEWLINE# #INDENT# _install_pkg ( env , dep , brew_cmd , ipkgs ) #NEWLINE# #UNINDENT# git_version = None #NEWLINE# with quiet ( ) : #NEWLINE# #INDENT# with settings ( warn_only = True ) : #NEWLINE# #INDENT# git_version = env . safe_run_output ( 'git --version' ) . strip ( ) . split ( ) [ ( - 1 ) ] #NEWLINE# #UNINDENT# #UNINDENT# if ( git_version and ( LooseVersion ( git_version ) < LooseVersion ( '1.7' ) ) ) : #NEWLINE# #INDENT# _install_pkg ( env , 'git' , brew_cmd , ipkgs ) #NEWLINE# #UNINDENT# for dep in [ 'sambamba' ] : #NEWLINE# #INDENT# env . safe_run ( '{brew_cmd} remove --force {dep}' . format ( ** locals ( ) ) ) #NEWLINE# #UNINDENT# for dependency in [ 'htslib' ] : #NEWLINE# #INDENT# if ( dependency in packages ) : #NEWLINE# #INDENT# if ( ( dependency in ipkgs [ 'outdated' ] ) or ( ( 'chapmanb/cbl/%s' % dependency ) in ipkgs [ 'outdated' ] ) or ( dependency not in ipkgs [ 'current' ] ) ) : #NEWLINE# #INDENT# _install_pkg_latest ( env , dependency , [ ] , brew_cmd , ipkgs ) #NEWLINE# #UNINDENT# #UNINDENT# #UNINDENT# if ( 'cpanminus' in packages ) : #NEWLINE# #INDENT# _install_pkg_latest ( env , 'cpanminus' , [ ] , brew_cmd , ipkgs ) #NEWLINE# _install_pkg_latest ( env , 'samtools-library-0.1' , [ ] , brew_cmd , ipkgs ) #NEWLINE# cpan . install_packages ( env ) #NEWLINE# #UNINDENT# if env . use_sudo : #NEWLINE# #INDENT# paths = [ 'share' , 'share/java' ] #NEWLINE# for path in paths : #NEWLINE# #INDENT# with quiet ( ) : #NEWLINE# #INDENT# test_access = env . safe_run ( ( 'test -d %s/%s && test -O %s/%s' % ( env . system_install , path , env . system_install , path ) ) ) #NEWLINE# #UNINDENT# if ( test_access . failed and env . safe_exists ( ( '%s/%s' % ( env . system_install , path ) ) ) ) : #NEWLINE# #INDENT# env . safe_sudo ( ( 'chown %s %s/%s' % ( env . user , env . system_install , path ) ) )