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Makefile
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# This Makefile is for the CGL extension to perl.
#
# It was generated automatically by MakeMaker version
# 6.17 (Revision: 1.133) from the contents of
# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
#
# ANY CHANGES MADE HERE WILL BE LOST!
#
# MakeMaker ARGV: ()
#
# MakeMaker Parameters:
# ABSTRACT => q[]
# AUTHOR => q[Mark Yandell ([email protected])]
# EXE_FILES => [q[script/cgl_version], q[script/cgl_tutorial], q[script/cgl_phat_tutorial], q[script/cgl_so_reasoner], q[script/cgl_compare_annotations], q[script/cgl_validate]]
# NAME => q[CGL]
# PREREQ_PM => { Test::More=>q[0], Test::Inline=>q[0], Bio::CodonUsage::Table=>q[0] }
# VERSION_FROM => q[lib/CGL/Version.pm]
# clean => { FILES=>q[t/embedded-*t pod2htm[di].tmp Makefile.PL~] }
# --- MakeMaker post_initialize section:
# --- MakeMaker const_config section:
# These definitions are from config.sh (via /System/Library/Perl/5.8.6/darwin-thread-multi-2level/Config.pm)
# They may have been overridden via Makefile.PL or on the command line
AR = ar
CC = cc
CCCDLFLAGS =
CCDLFLAGS =
DLEXT = bundle
DLSRC = dl_dlopen.xs
LD = env MACOSX_DEPLOYMENT_TARGET=10.3 cc
LDDLFLAGS = -bundle -undefined dynamic_lookup -L/usr/local/lib
LDFLAGS = -L/usr/local/lib
LIBC = /usr/lib/libc.dylib
LIB_EXT = .a
OBJ_EXT = .o
OSNAME = darwin
OSVERS = 8.0
RANLIB = /usr/bin/ar ts
SITELIBEXP = /Library/Perl/5.8.6
SITEARCHEXP = /Library/Perl/5.8.6/darwin-thread-multi-2level
SO = dylib
EXE_EXT =
FULL_AR = /usr/bin/ar
VENDORARCHEXP = /Network/Library/Perl/5.8.6/darwin-thread-multi-2level
VENDORLIBEXP = /Network/Library/Perl/5.8.6
# --- MakeMaker constants section:
AR_STATIC_ARGS = cr
DIRFILESEP = /
NAME = CGL
NAME_SYM = CGL
VERSION = 0.08
VERSION_MACRO = VERSION
VERSION_SYM = 0_08
DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
XS_VERSION = 0.08
XS_VERSION_MACRO = XS_VERSION
XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
INST_ARCHLIB = ../blib/arch
INST_SCRIPT = ../blib/script
INST_BIN = ../blib/bin
INST_LIB = ../blib/lib
INST_MAN1DIR = ../blib/man1
INST_MAN3DIR = ../blib/man3
MAN1EXT = 1
MAN3EXT = 3pm
INSTALLDIRS = site
DESTDIR =
PREFIX =
PERLPREFIX = /
SITEPREFIX = /usr/local
VENDORPREFIX = /usr/local
INSTALLPRIVLIB = $(PERLPREFIX)/System/Library/Perl/5.8.6
DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
INSTALLSITELIB = /Library/Perl/5.8.6
DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
INSTALLVENDORLIB = /Network/Library/Perl/5.8.6
DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
INSTALLARCHLIB = $(PERLPREFIX)/System/Library/Perl/5.8.6/darwin-thread-multi-2level
DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
INSTALLSITEARCH = /Library/Perl/5.8.6/darwin-thread-multi-2level
DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
INSTALLVENDORARCH = /Network/Library/Perl/5.8.6/darwin-thread-multi-2level
DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
INSTALLBIN = $(PERLPREFIX)/usr/bin
DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
INSTALLSITEBIN = $(SITEPREFIX)/bin
DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
INSTALLVENDORBIN = $(VENDORPREFIX)/bin
DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
INSTALLSCRIPT = $(PERLPREFIX)/usr/bin
DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
INSTALLMAN1DIR = $(PERLPREFIX)/usr/share/man/man1
DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1
DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/man/man1
DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
INSTALLMAN3DIR = $(PERLPREFIX)/usr/share/man/man3
DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3
DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/man/man3
DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
PERL_LIB = /System/Library/Perl/5.8.6
PERL_ARCHLIB = /System/Library/Perl/5.8.6/darwin-thread-multi-2level
LIBPERL_A = libperl.a
FIRST_MAKEFILE = Makefile
MAKEFILE_OLD = $(FIRST_MAKEFILE).old
MAKE_APERL_FILE = $(FIRST_MAKEFILE).aperl
PERLMAINCC = $(CC)
PERL_INC = /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE
PERL = /usr/bin/perl
FULLPERL = /usr/bin/perl
ABSPERL = $(PERL)
PERLRUN = $(PERL)
FULLPERLRUN = $(FULLPERL)
ABSPERLRUN = $(ABSPERL)
PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
PERL_CORE = 0
PERM_RW = 644
PERM_RWX = 755
MAKEMAKER = /System/Library/Perl/5.8.6/ExtUtils/MakeMaker.pm
MM_VERSION = 6.17
MM_REVISION = 1.133
# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
FULLEXT = CGL
BASEEXT = CGL
PARENT_NAME =
DLBASE = $(BASEEXT)
VERSION_FROM = lib/CGL/Version.pm
OBJECT =
LDFROM = $(OBJECT)
LINKTYPE = dynamic
# Handy lists of source code files:
XS_FILES =
C_FILES =
O_FILES =
H_FILES =
MAN1PODS = script/cgl_compare_annotations \
script/cgl_phat_tutorial \
script/cgl_so_reasoner \
script/cgl_tutorial \
script/cgl_version
MAN3PODS = PROTO.pm \
lib/Bio/Search/HSP/PhatHSP.pod \
lib/Bio/Search/HSP/PhatHSP/Base.pm \
lib/Bio/Search/HSP/PhatHSP/blastn.pm \
lib/Bio/Search/HSP/PhatHSP/blastp.pm \
lib/Bio/Search/HSP/PhatHSP/blastx.pm \
lib/Bio/Search/HSP/PhatHSP/tblastn.pm \
lib/Bio/Search/HSP/PhatHSP/tblastx.pm \
lib/Bio/Search/Hit/PhatHit.pod \
lib/Bio/Search/Hit/PhatHit/Base.pm \
lib/Bio/Search/Hit/PhatHit/blastn.pm \
lib/Bio/Search/Hit/PhatHit/blastp.pm \
lib/Bio/Search/Hit/PhatHit/blastx.pm \
lib/Bio/Search/Hit/PhatHit/tblastn.pm \
lib/Bio/Search/Hit/PhatHit/tblastx.pm \
lib/CGL.pod \
lib/CGL/Annotation.pm \
lib/CGL/Annotation/Feature.pm \
lib/CGL/Annotation/Feature/Contig.pm \
lib/CGL/Annotation/Feature/Exon.pm \
lib/CGL/Annotation/Feature/Gene.pm \
lib/CGL/Annotation/Feature/Intron.pm \
lib/CGL/Annotation/Feature/Protein.pm \
lib/CGL/Annotation/Feature/Transcript.pm \
lib/CGL/Annotation/FeatureLocation.pm \
lib/CGL/Annotation/FeatureRelationship.pm \
lib/CGL/Annotation/Iterator.pm \
lib/CGL/Annotation/Trace.pm \
lib/CGL/Clone.pm \
lib/CGL/Ontology/GO.pm \
lib/CGL/Ontology/Node.pm \
lib/CGL/Ontology/NodeRelationship.pm \
lib/CGL/Ontology/Ontology.pm \
lib/CGL/Ontology/Parser/OBO.pm \
lib/CGL/Ontology/SO.pm \
lib/CGL/Ontology/Trace.pm \
lib/CGL/Revcomp.pm \
lib/CGL/TranslationMachine.pm \
lib/CGL/Version.pm
# Where is the Config information that we are using/depend on
CONFIGDEP = $(PERL_ARCHLIB)$(DIRFILESEP)Config.pm $(PERL_INC)$(DIRFILESEP)config.h
# Where to build things
INST_LIBDIR = $(INST_LIB)
INST_ARCHLIBDIR = $(INST_ARCHLIB)
INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
INST_STATIC =
INST_DYNAMIC =
INST_BOOT =
# Extra linker info
EXPORT_LIST =
PERL_ARCHIVE =
PERL_ARCHIVE_AFTER =
TO_INST_PM = PROTO.pm \
lib/Bio/Search/HSP/PhatHSP.pod \
lib/Bio/Search/HSP/PhatHSP/Base.pm \
lib/Bio/Search/HSP/PhatHSP/blastn.pm \
lib/Bio/Search/HSP/PhatHSP/blastp.pm \
lib/Bio/Search/HSP/PhatHSP/blastx.pm \
lib/Bio/Search/HSP/PhatHSP/tblastn.pm \
lib/Bio/Search/HSP/PhatHSP/tblastx.pm \
lib/Bio/Search/Hit/PhatHit.pod \
lib/Bio/Search/Hit/PhatHit/Base.pm \
lib/Bio/Search/Hit/PhatHit/blastn.pm \
lib/Bio/Search/Hit/PhatHit/blastp.pm \
lib/Bio/Search/Hit/PhatHit/blastx.pm \
lib/Bio/Search/Hit/PhatHit/tblastn.pm \
lib/Bio/Search/Hit/PhatHit/tblastx.pm \
lib/CGL.pod \
lib/CGL/Annotation.pm \
lib/CGL/Annotation.pm_hold \
lib/CGL/Annotation/Feature.pm \
lib/CGL/Annotation/Feature/Contig.pm \
lib/CGL/Annotation/Feature/Exon.pm \
lib/CGL/Annotation/Feature/Gene.pm \
lib/CGL/Annotation/Feature/Intron.pm \
lib/CGL/Annotation/Feature/Protein.pm \
lib/CGL/Annotation/Feature/Sequence_variant.pm \
lib/CGL/Annotation/Feature/Transcript.pm \
lib/CGL/Annotation/FeatureLocation.pm \
lib/CGL/Annotation/FeatureRelationship.pm \
lib/CGL/Annotation/Iterator.pm \
lib/CGL/Annotation/Trace.pm \
lib/CGL/Clone.pm \
lib/CGL/Ontology/GO.pm \
lib/CGL/Ontology/Node.pm \
lib/CGL/Ontology/NodeRelationship.pm \
lib/CGL/Ontology/Ontology.pm \
lib/CGL/Ontology/Parser/OBO.pm \
lib/CGL/Ontology/SO.pm \
lib/CGL/Ontology/Trace.pm \
lib/CGL/Revcomp.pm \
lib/CGL/TranslationMachine.pm \
lib/CGL/Version.pm
PM_TO_BLIB = PROTO.pm \
$(INST_LIB)/PROTO.pm \
lib/CGL/Revcomp.pm \
../blib/lib/CGL/Revcomp.pm \
lib/Bio/Search/HSP/PhatHSP/blastn.pm \
../blib/lib/Bio/Search/HSP/PhatHSP/blastn.pm \
lib/CGL/Annotation/Feature/Intron.pm \
../blib/lib/CGL/Annotation/Feature/Intron.pm \
lib/CGL/Annotation/Feature/Gene.pm \
../blib/lib/CGL/Annotation/Feature/Gene.pm \
lib/CGL/Annotation.pm \
../blib/lib/CGL/Annotation.pm \
lib/CGL/Annotation/Iterator.pm \
../blib/lib/CGL/Annotation/Iterator.pm \
lib/CGL/Annotation.pm_hold \
../blib/lib/CGL/Annotation.pm_hold \
lib/CGL/Clone.pm \
../blib/lib/CGL/Clone.pm \
lib/Bio/Search/HSP/PhatHSP/blastp.pm \
../blib/lib/Bio/Search/HSP/PhatHSP/blastp.pm \
lib/CGL/Annotation/Feature/Contig.pm \
../blib/lib/CGL/Annotation/Feature/Contig.pm \
lib/Bio/Search/Hit/PhatHit.pod \
../blib/lib/Bio/Search/Hit/PhatHit.pod \
lib/Bio/Search/Hit/PhatHit/tblastn.pm \
../blib/lib/Bio/Search/Hit/PhatHit/tblastn.pm \
lib/CGL/Annotation/FeatureRelationship.pm \
../blib/lib/CGL/Annotation/FeatureRelationship.pm \
lib/CGL/TranslationMachine.pm \
../blib/lib/CGL/TranslationMachine.pm \
lib/CGL/Ontology/Parser/OBO.pm \
../blib/lib/CGL/Ontology/Parser/OBO.pm \
lib/CGL/Annotation/Feature.pm \
../blib/lib/CGL/Annotation/Feature.pm \
lib/Bio/Search/Hit/PhatHit/blastx.pm \
../blib/lib/Bio/Search/Hit/PhatHit/blastx.pm \
lib/CGL.pod \
../blib/lib/CGL.pod \
lib/Bio/Search/Hit/PhatHit/tblastx.pm \
../blib/lib/Bio/Search/Hit/PhatHit/tblastx.pm \
lib/CGL/Ontology/Trace.pm \
../blib/lib/CGL/Ontology/Trace.pm \
lib/CGL/Annotation/Feature/Transcript.pm \
../blib/lib/CGL/Annotation/Feature/Transcript.pm \
lib/Bio/Search/HSP/PhatHSP/Base.pm \
../blib/lib/Bio/Search/HSP/PhatHSP/Base.pm \
lib/Bio/Search/Hit/PhatHit/blastp.pm \
../blib/lib/Bio/Search/Hit/PhatHit/blastp.pm \
lib/CGL/Ontology/GO.pm \
../blib/lib/CGL/Ontology/GO.pm \
lib/CGL/Version.pm \
../blib/lib/CGL/Version.pm \
lib/Bio/Search/HSP/PhatHSP.pod \
../blib/lib/Bio/Search/HSP/PhatHSP.pod \
lib/CGL/Ontology/SO.pm \
../blib/lib/CGL/Ontology/SO.pm \
lib/CGL/Annotation/Feature/Protein.pm \
../blib/lib/CGL/Annotation/Feature/Protein.pm \
lib/Bio/Search/Hit/PhatHit/blastn.pm \
../blib/lib/Bio/Search/Hit/PhatHit/blastn.pm \
lib/Bio/Search/HSP/PhatHSP/tblastx.pm \
../blib/lib/Bio/Search/HSP/PhatHSP/tblastx.pm \
lib/CGL/Annotation/Feature/Exon.pm \
../blib/lib/CGL/Annotation/Feature/Exon.pm \
lib/CGL/Ontology/Ontology.pm \
../blib/lib/CGL/Ontology/Ontology.pm \
lib/CGL/Annotation/Trace.pm \
../blib/lib/CGL/Annotation/Trace.pm \
lib/Bio/Search/HSP/PhatHSP/tblastn.pm \
../blib/lib/Bio/Search/HSP/PhatHSP/tblastn.pm \
lib/CGL/Ontology/NodeRelationship.pm \
../blib/lib/CGL/Ontology/NodeRelationship.pm \
lib/CGL/Annotation/Feature/Sequence_variant.pm \
../blib/lib/CGL/Annotation/Feature/Sequence_variant.pm \
lib/CGL/Ontology/Node.pm \
../blib/lib/CGL/Ontology/Node.pm \
lib/Bio/Search/Hit/PhatHit/Base.pm \
../blib/lib/Bio/Search/Hit/PhatHit/Base.pm \
lib/Bio/Search/HSP/PhatHSP/blastx.pm \
../blib/lib/Bio/Search/HSP/PhatHSP/blastx.pm \
lib/CGL/Annotation/FeatureLocation.pm \
../blib/lib/CGL/Annotation/FeatureLocation.pm
# --- MakeMaker platform_constants section:
MM_Unix_VERSION = 1.42
PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
# --- MakeMaker tool_autosplit section:
# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
AUTOSPLITFILE = $(PERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)'
# --- MakeMaker tool_xsubpp section:
# --- MakeMaker tools_other section:
SHELL = /bin/sh
CHMOD = chmod
CP = cp
MV = mv
NOOP = $(SHELL) -c true
NOECHO = @
RM_F = rm -f
RM_RF = rm -rf
TEST_F = test -f
TOUCH = touch
UMASK_NULL = umask 0
DEV_NULL = > /dev/null 2>&1
MKPATH = $(PERLRUN) "-MExtUtils::Command" -e mkpath
EQUALIZE_TIMESTAMP = $(PERLRUN) "-MExtUtils::Command" -e eqtime
ECHO = echo
ECHO_N = echo -n
UNINST = 0
VERBINST = 0
MOD_INSTALL = $(PERLRUN) -MExtUtils::Install -e 'install({@ARGV}, '\''$(VERBINST)'\'', 0, '\''$(UNINST)'\'');'
DOC_INSTALL = $(PERLRUN) "-MExtUtils::Command::MM" -e perllocal_install
UNINSTALL = $(PERLRUN) "-MExtUtils::Command::MM" -e uninstall
WARN_IF_OLD_PACKLIST = $(PERLRUN) "-MExtUtils::Command::MM" -e warn_if_old_packlist
# --- MakeMaker makemakerdflt section:
makemakerdflt: all
$(NOECHO) $(NOOP)
# --- MakeMaker dist section skipped.
# --- MakeMaker macro section:
# --- MakeMaker depend section:
# --- MakeMaker cflags section:
# --- MakeMaker const_loadlibs section:
# --- MakeMaker const_cccmd section:
# --- MakeMaker post_constants section:
# --- MakeMaker pasthru section:
PASTHRU = LIB="$(LIB)"\
LIBPERL_A="$(LIBPERL_A)"\
LINKTYPE="$(LINKTYPE)"\
PREFIX="$(PREFIX)"\
OPTIMIZE="$(OPTIMIZE)"\
PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\
PASTHRU_INC="$(PASTHRU_INC)"
# --- MakeMaker special_targets section:
.SUFFIXES: .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
.PHONY: all config static dynamic test linkext manifest
# --- MakeMaker c_o section:
# --- MakeMaker xs_c section:
# --- MakeMaker xs_o section:
# --- MakeMaker top_targets section:
POD2TEST_EXE = pod2test
all :: pure_all manifypods
$(NOECHO) $(NOOP)
pure_all :: config pm_to_blib subdirs linkext testifypods
$(NOECHO) $(NOOP)
subdirs :: $(MYEXTLIB)
$(NOECHO) $(NOOP)
config :: $(FIRST_MAKEFILE) $(INST_LIBDIR)$(DIRFILESEP).exists
$(NOECHO) $(NOOP)
config :: $(INST_ARCHAUTODIR)$(DIRFILESEP).exists
$(NOECHO) $(NOOP)
config :: $(INST_AUTODIR)$(DIRFILESEP).exists
$(NOECHO) $(NOOP)
$(INST_AUTODIR)/.exists :: /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h
$(NOECHO) $(MKPATH) $(INST_AUTODIR)
$(NOECHO) $(EQUALIZE_TIMESTAMP) /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h $(INST_AUTODIR)/.exists
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_AUTODIR)
$(INST_LIBDIR)/.exists :: /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h
$(NOECHO) $(MKPATH) $(INST_LIBDIR)
$(NOECHO) $(EQUALIZE_TIMESTAMP) /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h $(INST_LIBDIR)/.exists
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_LIBDIR)
$(INST_ARCHAUTODIR)/.exists :: /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h
$(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
$(NOECHO) $(EQUALIZE_TIMESTAMP) /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h $(INST_ARCHAUTODIR)/.exists
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_ARCHAUTODIR)
config :: $(INST_MAN1DIR)$(DIRFILESEP).exists
$(NOECHO) $(NOOP)
$(INST_MAN1DIR)/.exists :: /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h
$(NOECHO) $(MKPATH) $(INST_MAN1DIR)
$(NOECHO) $(EQUALIZE_TIMESTAMP) /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h $(INST_MAN1DIR)/.exists
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_MAN1DIR)
config :: $(INST_MAN3DIR)$(DIRFILESEP).exists
$(NOECHO) $(NOOP)
$(INST_MAN3DIR)/.exists :: /System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE/perl.h
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help:
perldoc ExtUtils::MakeMaker
testifypods : t/embedded-script-cgl_version.t t/embedded-script-cgl_compare_annotations.t t/embedded-script-cgl_so_reasoner.t t/embedded-script-cgl_phat_tutorial.t t/embedded-script-cgl_tutorial.t t/embedded-PROTO.t t/embedded-CGL-Revcomp.t t/embedded-Bio-Search-HSP-PhatHSP-blastn.t t/embedded-CGL-Annotation-Feature-Intron.t t/embedded-CGL-Annotation-Feature-Gene.t t/embedded-CGL-Annotation.t t/embedded-CGL-Annotation-Iterator.t t/embedded-Bio-Search-HSP-PhatHSP-blastp.t t/embedded-CGL-Clone.t t/embedded-CGL-Annotation-Feature-Contig.t t/embedded-Bio-Search-Hit-PhatHit-tblastn.t t/embedded-Bio-Search-Hit-PhatHit.t t/embedded-CGL-TranslationMachine.t t/embedded-CGL-Annotation-FeatureRelationship.t t/embedded-CGL-Ontology-Parser-OBO.t t/embedded-CGL-Annotation-Feature.t t/embedded-Bio-Search-Hit-PhatHit-blastx.t t/embedded-CGL.t t/embedded-Bio-Search-Hit-PhatHit-tblastx.t t/embedded-CGL-Ontology-Trace.t t/embedded-CGL-Annotation-Feature-Transcript.t t/embedded-Bio-Search-HSP-PhatHSP-Base.t t/embedded-Bio-Search-Hit-PhatHit-blastp.t t/embedded-CGL-Ontology-GO.t t/embedded-CGL-Version.t t/embedded-Bio-Search-HSP-PhatHSP.t t/embedded-CGL-Ontology-SO.t t/embedded-CGL-Annotation-Feature-Protein.t t/embedded-Bio-Search-Hit-PhatHit-blastn.t t/embedded-CGL-Annotation-Feature-Exon.t t/embedded-Bio-Search-HSP-PhatHSP-tblastx.t t/embedded-CGL-Ontology-Ontology.t t/embedded-CGL-Annotation-Trace.t t/embedded-Bio-Search-HSP-PhatHSP-tblastn.t t/embedded-CGL-Ontology-NodeRelationship.t t/embedded-CGL-Ontology-Node.t t/embedded-Bio-Search-Hit-PhatHit-Base.t t/embedded-Bio-Search-HSP-PhatHSP-blastx.t t/embedded-CGL-Annotation-FeatureLocation.t
t/embedded-script-cgl_version.t : script/cgl_version
-$(POD2TEST_EXE) script/cgl_version t/embedded-script-cgl_version.t
t/embedded-script-cgl_compare_annotations.t : script/cgl_compare_annotations
-$(POD2TEST_EXE) script/cgl_compare_annotations t/embedded-script-cgl_compare_annotations.t
t/embedded-script-cgl_so_reasoner.t : script/cgl_so_reasoner
-$(POD2TEST_EXE) script/cgl_so_reasoner t/embedded-script-cgl_so_reasoner.t
t/embedded-script-cgl_phat_tutorial.t : script/cgl_phat_tutorial
-$(POD2TEST_EXE) script/cgl_phat_tutorial t/embedded-script-cgl_phat_tutorial.t
t/embedded-script-cgl_tutorial.t : script/cgl_tutorial
-$(POD2TEST_EXE) script/cgl_tutorial t/embedded-script-cgl_tutorial.t
t/embedded-PROTO.t : PROTO.pm
-$(POD2TEST_EXE) PROTO.pm t/embedded-PROTO.t
t/embedded-CGL-Revcomp.t : lib/CGL/Revcomp.pm
-$(POD2TEST_EXE) lib/CGL/Revcomp.pm t/embedded-CGL-Revcomp.t
t/embedded-Bio-Search-HSP-PhatHSP-blastn.t : lib/Bio/Search/HSP/PhatHSP/blastn.pm
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP/blastn.pm t/embedded-Bio-Search-HSP-PhatHSP-blastn.t
t/embedded-CGL-Annotation-Feature-Intron.t : lib/CGL/Annotation/Feature/Intron.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature/Intron.pm t/embedded-CGL-Annotation-Feature-Intron.t
t/embedded-CGL-Annotation-Feature-Gene.t : lib/CGL/Annotation/Feature/Gene.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature/Gene.pm t/embedded-CGL-Annotation-Feature-Gene.t
t/embedded-CGL-Annotation.t : lib/CGL/Annotation.pm
-$(POD2TEST_EXE) lib/CGL/Annotation.pm t/embedded-CGL-Annotation.t
t/embedded-CGL-Annotation-Iterator.t : lib/CGL/Annotation/Iterator.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Iterator.pm t/embedded-CGL-Annotation-Iterator.t
t/embedded-Bio-Search-HSP-PhatHSP-blastp.t : lib/Bio/Search/HSP/PhatHSP/blastp.pm
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP/blastp.pm t/embedded-Bio-Search-HSP-PhatHSP-blastp.t
t/embedded-CGL-Clone.t : lib/CGL/Clone.pm
-$(POD2TEST_EXE) lib/CGL/Clone.pm t/embedded-CGL-Clone.t
t/embedded-CGL-Annotation-Feature-Contig.t : lib/CGL/Annotation/Feature/Contig.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature/Contig.pm t/embedded-CGL-Annotation-Feature-Contig.t
t/embedded-Bio-Search-Hit-PhatHit-tblastn.t : lib/Bio/Search/Hit/PhatHit/tblastn.pm
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit/tblastn.pm t/embedded-Bio-Search-Hit-PhatHit-tblastn.t
t/embedded-Bio-Search-Hit-PhatHit.t : lib/Bio/Search/Hit/PhatHit.pod
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit.pod t/embedded-Bio-Search-Hit-PhatHit.t
t/embedded-CGL-TranslationMachine.t : lib/CGL/TranslationMachine.pm
-$(POD2TEST_EXE) lib/CGL/TranslationMachine.pm t/embedded-CGL-TranslationMachine.t
t/embedded-CGL-Annotation-FeatureRelationship.t : lib/CGL/Annotation/FeatureRelationship.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/FeatureRelationship.pm t/embedded-CGL-Annotation-FeatureRelationship.t
t/embedded-CGL-Ontology-Parser-OBO.t : lib/CGL/Ontology/Parser/OBO.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/Parser/OBO.pm t/embedded-CGL-Ontology-Parser-OBO.t
t/embedded-CGL-Annotation-Feature.t : lib/CGL/Annotation/Feature.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature.pm t/embedded-CGL-Annotation-Feature.t
t/embedded-Bio-Search-Hit-PhatHit-blastx.t : lib/Bio/Search/Hit/PhatHit/blastx.pm
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit/blastx.pm t/embedded-Bio-Search-Hit-PhatHit-blastx.t
t/embedded-CGL.t : lib/CGL.pod
-$(POD2TEST_EXE) lib/CGL.pod t/embedded-CGL.t
t/embedded-Bio-Search-Hit-PhatHit-tblastx.t : lib/Bio/Search/Hit/PhatHit/tblastx.pm
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit/tblastx.pm t/embedded-Bio-Search-Hit-PhatHit-tblastx.t
t/embedded-CGL-Ontology-Trace.t : lib/CGL/Ontology/Trace.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/Trace.pm t/embedded-CGL-Ontology-Trace.t
t/embedded-CGL-Annotation-Feature-Transcript.t : lib/CGL/Annotation/Feature/Transcript.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature/Transcript.pm t/embedded-CGL-Annotation-Feature-Transcript.t
t/embedded-Bio-Search-HSP-PhatHSP-Base.t : lib/Bio/Search/HSP/PhatHSP/Base.pm
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP/Base.pm t/embedded-Bio-Search-HSP-PhatHSP-Base.t
t/embedded-Bio-Search-Hit-PhatHit-blastp.t : lib/Bio/Search/Hit/PhatHit/blastp.pm
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit/blastp.pm t/embedded-Bio-Search-Hit-PhatHit-blastp.t
t/embedded-CGL-Ontology-GO.t : lib/CGL/Ontology/GO.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/GO.pm t/embedded-CGL-Ontology-GO.t
t/embedded-CGL-Version.t : lib/CGL/Version.pm
-$(POD2TEST_EXE) lib/CGL/Version.pm t/embedded-CGL-Version.t
t/embedded-Bio-Search-HSP-PhatHSP.t : lib/Bio/Search/HSP/PhatHSP.pod
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP.pod t/embedded-Bio-Search-HSP-PhatHSP.t
t/embedded-CGL-Ontology-SO.t : lib/CGL/Ontology/SO.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/SO.pm t/embedded-CGL-Ontology-SO.t
t/embedded-CGL-Annotation-Feature-Protein.t : lib/CGL/Annotation/Feature/Protein.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature/Protein.pm t/embedded-CGL-Annotation-Feature-Protein.t
t/embedded-Bio-Search-Hit-PhatHit-blastn.t : lib/Bio/Search/Hit/PhatHit/blastn.pm
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit/blastn.pm t/embedded-Bio-Search-Hit-PhatHit-blastn.t
t/embedded-CGL-Annotation-Feature-Exon.t : lib/CGL/Annotation/Feature/Exon.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Feature/Exon.pm t/embedded-CGL-Annotation-Feature-Exon.t
t/embedded-Bio-Search-HSP-PhatHSP-tblastx.t : lib/Bio/Search/HSP/PhatHSP/tblastx.pm
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP/tblastx.pm t/embedded-Bio-Search-HSP-PhatHSP-tblastx.t
t/embedded-CGL-Ontology-Ontology.t : lib/CGL/Ontology/Ontology.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/Ontology.pm t/embedded-CGL-Ontology-Ontology.t
t/embedded-CGL-Annotation-Trace.t : lib/CGL/Annotation/Trace.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/Trace.pm t/embedded-CGL-Annotation-Trace.t
t/embedded-Bio-Search-HSP-PhatHSP-tblastn.t : lib/Bio/Search/HSP/PhatHSP/tblastn.pm
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP/tblastn.pm t/embedded-Bio-Search-HSP-PhatHSP-tblastn.t
t/embedded-CGL-Ontology-NodeRelationship.t : lib/CGL/Ontology/NodeRelationship.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/NodeRelationship.pm t/embedded-CGL-Ontology-NodeRelationship.t
t/embedded-CGL-Ontology-Node.t : lib/CGL/Ontology/Node.pm
-$(POD2TEST_EXE) lib/CGL/Ontology/Node.pm t/embedded-CGL-Ontology-Node.t
t/embedded-Bio-Search-Hit-PhatHit-Base.t : lib/Bio/Search/Hit/PhatHit/Base.pm
-$(POD2TEST_EXE) lib/Bio/Search/Hit/PhatHit/Base.pm t/embedded-Bio-Search-Hit-PhatHit-Base.t
t/embedded-Bio-Search-HSP-PhatHSP-blastx.t : lib/Bio/Search/HSP/PhatHSP/blastx.pm
-$(POD2TEST_EXE) lib/Bio/Search/HSP/PhatHSP/blastx.pm t/embedded-Bio-Search-HSP-PhatHSP-blastx.t
t/embedded-CGL-Annotation-FeatureLocation.t : lib/CGL/Annotation/FeatureLocation.pm
-$(POD2TEST_EXE) lib/CGL/Annotation/FeatureLocation.pm t/embedded-CGL-Annotation-FeatureLocation.t
# --- MakeMaker linkext section:
linkext :: $(LINKTYPE)
$(NOECHO) $(NOOP)
# --- MakeMaker dlsyms section:
# --- MakeMaker dynamic section:
dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
$(NOECHO) $(NOOP)
# --- MakeMaker dynamic_bs section:
BOOTSTRAP =
# --- MakeMaker dynamic_lib section:
# --- MakeMaker static section:
## $(INST_PM) has been moved to the all: target.
## It remains here for awhile to allow for old usage: "make static"
static :: $(FIRST_MAKEFILE) $(INST_STATIC)
$(NOECHO) $(NOOP)
# --- MakeMaker static_lib section:
# --- MakeMaker manifypods section:
POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
POD2MAN = $(POD2MAN_EXE)
manifypods : pure_all \
script/cgl_version \
script/cgl_compare_annotations \
script/cgl_so_reasoner \
script/cgl_phat_tutorial \
script/cgl_tutorial \
PROTO.pm \
lib/CGL/Revcomp.pm \
lib/Bio/Search/HSP/PhatHSP/blastn.pm \
lib/CGL/Annotation/Feature/Intron.pm \
lib/CGL/Annotation/Feature/Gene.pm \
lib/CGL/Annotation.pm \
lib/CGL/Annotation/Iterator.pm \
lib/Bio/Search/HSP/PhatHSP/blastp.pm \
lib/CGL/Clone.pm \
lib/CGL/Annotation/Feature/Contig.pm \
lib/Bio/Search/Hit/PhatHit/tblastn.pm \
lib/Bio/Search/Hit/PhatHit.pod \
lib/CGL/TranslationMachine.pm \
lib/CGL/Annotation/FeatureRelationship.pm \
lib/CGL/Ontology/Parser/OBO.pm \
lib/CGL/Annotation/Feature.pm \
lib/Bio/Search/Hit/PhatHit/blastx.pm \
lib/CGL.pod \
lib/Bio/Search/Hit/PhatHit/tblastx.pm \
lib/CGL/Ontology/Trace.pm \
lib/CGL/Annotation/Feature/Transcript.pm \
lib/Bio/Search/HSP/PhatHSP/Base.pm \
lib/Bio/Search/Hit/PhatHit/blastp.pm \
lib/CGL/Ontology/GO.pm \
lib/CGL/Version.pm \
lib/Bio/Search/HSP/PhatHSP.pod \
lib/CGL/Ontology/SO.pm \
lib/CGL/Annotation/Feature/Protein.pm \
lib/Bio/Search/Hit/PhatHit/blastn.pm \
lib/CGL/Annotation/Feature/Exon.pm \
lib/Bio/Search/HSP/PhatHSP/tblastx.pm \
lib/CGL/Ontology/Ontology.pm \
lib/CGL/Annotation/Trace.pm \
lib/Bio/Search/HSP/PhatHSP/tblastn.pm \
lib/CGL/Ontology/NodeRelationship.pm \
lib/CGL/Ontology/Node.pm \
lib/Bio/Search/Hit/PhatHit/Base.pm \
lib/Bio/Search/HSP/PhatHSP/blastx.pm \
lib/CGL/Annotation/FeatureLocation.pm \
PROTO.pm \
lib/CGL/Revcomp.pm \
lib/Bio/Search/HSP/PhatHSP/blastn.pm \
lib/CGL/Annotation/Feature/Intron.pm \
lib/CGL/Annotation/Feature/Gene.pm \
lib/CGL/Annotation.pm \
lib/CGL/Annotation/Iterator.pm \
lib/Bio/Search/HSP/PhatHSP/blastp.pm \
lib/CGL/Clone.pm \
lib/CGL/Annotation/Feature/Contig.pm \
lib/Bio/Search/Hit/PhatHit/tblastn.pm \
lib/Bio/Search/Hit/PhatHit.pod \
lib/CGL/TranslationMachine.pm \
lib/CGL/Annotation/FeatureRelationship.pm \
lib/CGL/Ontology/Parser/OBO.pm \
lib/CGL/Annotation/Feature.pm \
lib/Bio/Search/Hit/PhatHit/blastx.pm \
lib/CGL.pod \
lib/Bio/Search/Hit/PhatHit/tblastx.pm \
lib/CGL/Ontology/Trace.pm \
lib/CGL/Annotation/Feature/Transcript.pm \
lib/Bio/Search/HSP/PhatHSP/Base.pm \
lib/Bio/Search/Hit/PhatHit/blastp.pm \
lib/CGL/Ontology/GO.pm \
lib/CGL/Version.pm \
lib/Bio/Search/HSP/PhatHSP.pod \
lib/CGL/Ontology/SO.pm \
lib/CGL/Annotation/Feature/Protein.pm \
lib/Bio/Search/Hit/PhatHit/blastn.pm \
lib/CGL/Annotation/Feature/Exon.pm \
lib/Bio/Search/HSP/PhatHSP/tblastx.pm \
lib/CGL/Ontology/Ontology.pm \
lib/CGL/Annotation/Trace.pm \
lib/Bio/Search/HSP/PhatHSP/tblastn.pm \
lib/CGL/Ontology/NodeRelationship.pm \
lib/CGL/Ontology/Node.pm \
lib/Bio/Search/Hit/PhatHit/Base.pm \
lib/Bio/Search/HSP/PhatHSP/blastx.pm \
lib/CGL/Annotation/FeatureLocation.pm
$(NOECHO) $(POD2MAN) --section=1 --perm_rw=$(PERM_RW)\
script/cgl_version $(INST_MAN1DIR)/cgl_version.$(MAN1EXT) \
script/cgl_compare_annotations $(INST_MAN1DIR)/cgl_compare_annotations.$(MAN1EXT) \
script/cgl_so_reasoner $(INST_MAN1DIR)/cgl_so_reasoner.$(MAN1EXT) \
script/cgl_phat_tutorial $(INST_MAN1DIR)/cgl_phat_tutorial.$(MAN1EXT) \
script/cgl_tutorial $(INST_MAN1DIR)/cgl_tutorial.$(MAN1EXT)
$(NOECHO) $(POD2MAN) --section=3 --perm_rw=$(PERM_RW)\
PROTO.pm $(INST_MAN3DIR)/PROTO.$(MAN3EXT) \
lib/CGL/Revcomp.pm $(INST_MAN3DIR)/CGL::Revcomp.$(MAN3EXT) \
lib/Bio/Search/HSP/PhatHSP/blastn.pm $(INST_MAN3DIR)/Bio::Search::HSP::PhatHSP::blastn.$(MAN3EXT) \
lib/CGL/Annotation/Feature/Intron.pm $(INST_MAN3DIR)/CGL::Annotation::Feature::Intron.$(MAN3EXT) \
lib/CGL/Annotation/Feature/Gene.pm $(INST_MAN3DIR)/CGL::Annotation::Feature::Gene.$(MAN3EXT) \
lib/CGL/Annotation.pm $(INST_MAN3DIR)/CGL::Annotation.$(MAN3EXT) \
lib/CGL/Annotation/Iterator.pm $(INST_MAN3DIR)/CGL::Annotation::Iterator.$(MAN3EXT) \
lib/Bio/Search/HSP/PhatHSP/blastp.pm $(INST_MAN3DIR)/Bio::Search::HSP::PhatHSP::blastp.$(MAN3EXT) \
lib/CGL/Clone.pm $(INST_MAN3DIR)/CGL::Clone.$(MAN3EXT) \
lib/CGL/Annotation/Feature/Contig.pm $(INST_MAN3DIR)/CGL::Annotation::Feature::Contig.$(MAN3EXT) \
lib/Bio/Search/Hit/PhatHit/tblastn.pm $(INST_MAN3DIR)/Bio::Search::Hit::PhatHit::tblastn.$(MAN3EXT) \
lib/Bio/Search/Hit/PhatHit.pod $(INST_MAN3DIR)/Bio::Search::Hit::PhatHit.$(MAN3EXT) \
lib/CGL/TranslationMachine.pm $(INST_MAN3DIR)/CGL::TranslationMachine.$(MAN3EXT) \
lib/CGL/Annotation/FeatureRelationship.pm $(INST_MAN3DIR)/CGL::Annotation::FeatureRelationship.$(MAN3EXT) \
lib/CGL/Ontology/Parser/OBO.pm $(INST_MAN3DIR)/CGL::Ontology::Parser::OBO.$(MAN3EXT) \
lib/CGL/Annotation/Feature.pm $(INST_MAN3DIR)/CGL::Annotation::Feature.$(MAN3EXT) \
lib/Bio/Search/Hit/PhatHit/blastx.pm $(INST_MAN3DIR)/Bio::Search::Hit::PhatHit::blastx.$(MAN3EXT) \
lib/CGL.pod $(INST_MAN3DIR)/CGL.$(MAN3EXT) \
lib/Bio/Search/Hit/PhatHit/tblastx.pm $(INST_MAN3DIR)/Bio::Search::Hit::PhatHit::tblastx.$(MAN3EXT) \
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# --- MakeMaker subdirs section:
# none
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$(NOECHO) $(NOOP)
# --- MakeMaker clean section:
# Delete temporary files but do not touch installed files. We don't delete
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$(RM_F) ../blib/lib/CGL/Ontology/GO.pm ../blib/lib/Bio/Search/Hit/PhatHit/Base.pm ../blib/lib/CGL/Version.pm ../blib/lib/CGL/Annotation/Feature/Protein.pm ../blib/lib/Bio/Search/Hit/PhatHit/tblastn.pm
$(RM_F) ../blib/lib/CGL/Annotation/Trace.pm ../blib/lib/Bio/Search/HSP/PhatHSP/tblastx.pm ../blib/lib/CGL/Ontology/Parser/OBO.pm ../blib/lib/CGL/Ontology/Node.pm ../blib/lib/CGL/Ontology/NodeRelationship.pm
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# --- MakeMaker metafile section:
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$(NOECHO) $(ECHO) '#XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX#' >> META.yml
$(NOECHO) $(ECHO) 'name: CGL' >> META.yml
$(NOECHO) $(ECHO) 'version: 0.08' >> META.yml
$(NOECHO) $(ECHO) 'version_from: lib/CGL/Version.pm' >> META.yml
$(NOECHO) $(ECHO) 'installdirs: site' >> META.yml
$(NOECHO) $(ECHO) 'requires:' >> META.yml
$(NOECHO) $(ECHO) ' Bio::CodonUsage::Table: 0' >> META.yml
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# --- MakeMaker dist_basics section skipped.
# --- MakeMaker dist_core section skipped.
# --- MakeMaker distdir section skipped.
# --- MakeMaker dist_test section skipped.
# --- MakeMaker dist_ci section skipped.
# --- MakeMaker install section skipped.
# --- MakeMaker force section:
# Phony target to force checking subdirectories.
FORCE:
$(NOECHO) $(NOOP)
# --- MakeMaker perldepend section:
# --- MakeMaker makefile section:
# We take a very conservative approach here, but it's worth it.
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$(PERLRUN) Makefile.PL
$(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
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false
# --- MakeMaker staticmake section:
# --- MakeMaker makeaperl section ---
MAP_TARGET = ../perl
FULLPERL = /usr/bin/perl
# --- MakeMaker test section:
TEST_VERBOSE=0
TEST_TYPE=test_$(LINKTYPE)
TEST_FILE = test.pl
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# --- MakeMaker ppd section:
# Creates a PPD (Perl Package Description) for a binary distribution.
ppd:
$(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="0,08,0,0">' > $(DISTNAME).ppd
$(NOECHO) $(ECHO) ' <TITLE>$(DISTNAME)</TITLE>' >> $(DISTNAME).ppd
$(NOECHO) $(ECHO) ' <ABSTRACT></ABSTRACT>' >> $(DISTNAME).ppd
$(NOECHO) $(ECHO) ' <AUTHOR>Mark Yandell ([email protected])</AUTHOR>' >> $(DISTNAME).ppd
$(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
$(NOECHO) $(ECHO) ' <DEPENDENCY NAME="Bio-CodonUsage-Table" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
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# --- MakeMaker pm_to_blib section:
pm_to_blib: $(TO_INST_PM)
$(NOECHO) $(PERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', '\''$(PM_FILTER)'\'')'\
PROTO.pm $(INST_LIB)/PROTO.pm \
lib/CGL/Revcomp.pm ../blib/lib/CGL/Revcomp.pm \
lib/Bio/Search/HSP/PhatHSP/blastn.pm ../blib/lib/Bio/Search/HSP/PhatHSP/blastn.pm \
lib/CGL/Annotation/Feature/Intron.pm ../blib/lib/CGL/Annotation/Feature/Intron.pm \
lib/CGL/Annotation/Feature/Gene.pm ../blib/lib/CGL/Annotation/Feature/Gene.pm \
lib/CGL/Annotation.pm ../blib/lib/CGL/Annotation.pm \
lib/CGL/Annotation/Iterator.pm ../blib/lib/CGL/Annotation/Iterator.pm \
lib/CGL/Annotation.pm_hold ../blib/lib/CGL/Annotation.pm_hold \
lib/CGL/Clone.pm ../blib/lib/CGL/Clone.pm \
lib/Bio/Search/HSP/PhatHSP/blastp.pm ../blib/lib/Bio/Search/HSP/PhatHSP/blastp.pm \
lib/CGL/Annotation/Feature/Contig.pm ../blib/lib/CGL/Annotation/Feature/Contig.pm \
lib/Bio/Search/Hit/PhatHit.pod ../blib/lib/Bio/Search/Hit/PhatHit.pod \
lib/Bio/Search/Hit/PhatHit/tblastn.pm ../blib/lib/Bio/Search/Hit/PhatHit/tblastn.pm \
lib/CGL/Annotation/FeatureRelationship.pm ../blib/lib/CGL/Annotation/FeatureRelationship.pm \
lib/CGL/TranslationMachine.pm ../blib/lib/CGL/TranslationMachine.pm \
lib/CGL/Ontology/Parser/OBO.pm ../blib/lib/CGL/Ontology/Parser/OBO.pm \
lib/CGL/Annotation/Feature.pm ../blib/lib/CGL/Annotation/Feature.pm \
lib/Bio/Search/Hit/PhatHit/blastx.pm ../blib/lib/Bio/Search/Hit/PhatHit/blastx.pm \
lib/CGL.pod ../blib/lib/CGL.pod \
lib/Bio/Search/Hit/PhatHit/tblastx.pm ../blib/lib/Bio/Search/Hit/PhatHit/tblastx.pm \
lib/CGL/Ontology/Trace.pm ../blib/lib/CGL/Ontology/Trace.pm \
lib/CGL/Annotation/Feature/Transcript.pm ../blib/lib/CGL/Annotation/Feature/Transcript.pm \
lib/Bio/Search/HSP/PhatHSP/Base.pm ../blib/lib/Bio/Search/HSP/PhatHSP/Base.pm \