[Bioperl-l] Problems with BioPerl-1.4

Wolf-Gerolf Thies thies at itg.fzk.de
Mon Mar 1 11:40:29 EST 2004


Dear BioPerl experts,

I have tried to install BioPerl-1.4 on on True64UNIX (OSF-1) Version 5.1.
The standard make fails with the error:

 Make: line too long.  Stop.

Then I have tested the gnu make, but it also fails:

# /usr/local/bin/make
mkdir blib
mkdir blib/lib
mkdir blib/arch
mkdir blib/arch/auto
mkdir blib/arch/auto/Bio
mkdir blib/lib/auto
mkdir blib/lib/auto/Bio
mkdir blib/man1
mkdir blib/man3
make: execvp: /bin/sh: Arg list too long
make: *** [pm_to_blib] Error 127

Do you have any idea what might be my problem ? I join the makefile
to this mail.

With kind regards

Wolf-Gerolf Thies
-------------- next part --------------
# This Makefile is for the Bio extension to perl.
#
# It was generated automatically by MakeMaker version
# 5.45 (Revision: 1.222) 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[Bioinformatics Toolkit]
#	AUTHOR => q[Bioperl Team (bioperl-l at bioperl.org)]
#	DIR => []
#	DISTNAME => q[bioperl]
#	EXE_FILES => [q[./scripts_temp/bp_load_gff.pl], q[./scripts_temp/bp_genbank2gff.pl], q[./scripts_temp/bp_bulk_load_gff.pl], q[./scripts_temp/bp_fast_load_gff.pl], q[./scripts_temp/bp_generate_histogram.pl], q[./scripts_temp/bp_pg_bulk_load_gff.pl], q[./scripts_temp/bp_process_gadfly.pl], q[./scripts_temp/bp_process_ncbi_human.pl], q[./scripts_temp/bp_process_sgd.pl], q[./scripts_temp/bp_process_wormbase.pl], q[./scripts_temp/bp_biofetch_genbank_proxy.pl], q[./scripts_temp/bp_bioflat_index.pl], q[./scripts_temp/bp_biogetseq.pl], q[./scripts_temp/bp_flanks.pl], q[./scripts_temp/bp_biblio.pl], q[./scripts_temp/bp_frend.pl], q[./scripts_temp/bp_feature_draw.pl], q[./scripts_temp/bp_search_overview.pl], q[./scripts_temp/bp_fetch.pl], q[./scripts_temp/bp_index.pl], q[./scripts_temp/bp_composite_LD.pl], q[./scripts_temp/bp_heterogeneity_test.pl], q[./scripts_temp/bp_filter_search.pl], q[./scripts_temp/bp_extract_feature_seq.pl], q[./scripts_temp/bp_seqconvert.pl], q[./scripts_temp/bp_split_seq.pl], q[./scripts_temp/bp_translate_seq.pl], q[./scripts_temp/bp_aacomp.pl], q[./scripts_temp/bp_chaos_plot.pl], q[./scripts_temp/bp_gccalc.pl], q[./scripts_temp/bp_oligo_count.pl], q[./scripts_temp/bp_local_taxonomydb_query.pl], q[./scripts_temp/bp_taxid4species.pl], q[./scripts_temp/bp_blast2tree.pl], q[./scripts_temp/bp_nrdb.pl], q[./scripts_temp/bp_mrtrans.pl], q[./scripts_temp/bp_sreformat.pl], q[./scripts_temp/bp_dbsplit.pl], q[./scripts_temp/bp_mask_by_search.pl], q[./scripts_temp/bp_mutate.pl], q[./scripts_temp/bp_pairwise_kaks.pl], q[./scripts_temp/bp_remote_blast.pl], q[./scripts_temp/bp_search2BSML.pl], q[./scripts_temp/bp_search2alnblocks.pl], q[./scripts_temp/bp_search2gff.pl], q[./scripts_temp/bp_search2tribe.pl], q[./scripts_temp/bp_seq_length.pl]]
#	NAME => q[Bio]
#	PL_FILES => { doc/makedoc.PL=>[q[bioscripts.pod], q[biodatabases.pod], q[biodesign.pod], q[bioperl.pod]] }
#	PREREQ_PM => { HTML::Entities=>q[0], File::Spec=>q[0], File::Temp=>q[0], DB_File=>q[0], IO::Scalar=>q[0], IO::String=>q[0] }
#	VERSION_FROM => q[Bio/Root/Version.pm]
#	dist => { DIST_DEFAULT=>q[all tardist], COMPRESS=>q[gzip -9f], SUFFIX=>q[.gz] }
#	realclean => { FILES=>q[./Seq.pm.bak] }

# --- MakeMaker post_initialize section:


# --- MakeMaker const_config section:

# These definitions are from config.sh (via /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/Config.pm)

# They may have been overridden via Makefile.PL or on the command line
AR = ar
CC = cc
CCCDLFLAGS =  
CCDLFLAGS =   -Wl,-rpath,/usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE
DLEXT = so
DLSRC = dl_dlopen.xs
LD = ld
LDDLFLAGS = -shared -expect_unresolved "*" -O4 -msym -std -s
LDFLAGS = 
LIBC = /usr/shlib/libc.so
LIB_EXT = .a
OBJ_EXT = .o
OSNAME = dec_osf
OSVERS = 5.1
RANLIB = :
SO = so
EXE_EXT = 
FULL_AR = /usr/bin/ar


# --- MakeMaker constants section:
AR_STATIC_ARGS = cr
NAME = Bio
DISTNAME = bioperl
NAME_SYM = Bio
VERSION = 1.4
VERSION_SYM = 1_4
XS_VERSION = 1.4
INST_BIN = blib/bin
INST_EXE = blib/script
INST_LIB = blib/lib
INST_ARCHLIB = blib/arch
INST_SCRIPT = blib/script
PREFIX = /usr/lib/perl-5.6.0
INSTALLDIRS = site
INSTALLPRIVLIB = $(PREFIX)/lib/5.6.0
INSTALLARCHLIB = $(PREFIX)/lib/5.6.0/alpha-dec_osf
INSTALLSITELIB = $(PREFIX)/lib/site_perl/5.6.0
INSTALLSITEARCH = $(PREFIX)/lib/site_perl/5.6.0/alpha-dec_osf
INSTALLBIN = $(PREFIX)/bin
INSTALLSCRIPT = $(PREFIX)/bin
PERL_LIB = /usr/lib/perl-5.6.0/lib/5.6.0
PERL_ARCHLIB = /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf
SITELIBEXP = /usr/lib/perl-5.6.0/lib/site_perl/5.6.0
SITEARCHEXP = /usr/lib/perl-5.6.0/lib/site_perl/5.6.0/alpha-dec_osf
LIBPERL_A = libperl.a
FIRST_MAKEFILE = Makefile
MAKE_APERL_FILE = Makefile.aperl
PERLMAINCC = $(CC)
PERL_INC = /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE
PERL = /usr/bin/perl
FULLPERL = /usr/bin/perl
FULL_AR = /usr/bin/ar

VERSION_MACRO = VERSION
DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
XS_VERSION_MACRO = XS_VERSION
XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc

MAKEMAKER = /usr/lib/perl-5.6.0/lib/5.6.0/ExtUtils/MakeMaker.pm
MM_VERSION = 5.45

# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
# ROOTEXT = Directory part of FULLEXT with leading slash (eg /DBD)  !!! Deprecated from MM 5.32  !!!
# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
# DLBASE  = Basename part of dynamic library. May be just equal BASEEXT.
FULLEXT = Bio
BASEEXT = Bio
DLBASE = $(BASEEXT)
VERSION_FROM = Bio/Root/Version.pm
OBJECT = 
LDFROM = $(OBJECT)
LINKTYPE = dynamic

# Handy lists of source code files:
XS_FILES= 
C_FILES = 
O_FILES = 
H_FILES = 
HTMLLIBPODS    = 
HTMLSCRIPTPODS = 
MAN1PODS = ./scripts_temp/bp_aacomp.pl \
	./scripts_temp/bp_biblio.pl \
	./scripts_temp/bp_biofetch_genbank_proxy.pl \
	./scripts_temp/bp_biogetseq.pl \
	./scripts_temp/bp_blast2tree.pl \
	./scripts_temp/bp_bulk_load_gff.pl \
	./scripts_temp/bp_chaos_plot.pl \
	./scripts_temp/bp_composite_LD.pl \
	./scripts_temp/bp_dbsplit.pl \
	./scripts_temp/bp_extract_feature_seq.pl \
	./scripts_temp/bp_fast_load_gff.pl \
	./scripts_temp/bp_feature_draw.pl \
	./scripts_temp/bp_fetch.pl \
	./scripts_temp/bp_filter_search.pl \
	./scripts_temp/bp_flanks.pl \
	./scripts_temp/bp_frend.pl \
	./scripts_temp/bp_gccalc.pl \
	./scripts_temp/bp_genbank2gff.pl \
	./scripts_temp/bp_generate_histogram.pl \
	./scripts_temp/bp_heterogeneity_test.pl \
	./scripts_temp/bp_index.pl \
	./scripts_temp/bp_load_gff.pl \
	./scripts_temp/bp_local_taxonomydb_query.pl \
	./scripts_temp/bp_mask_by_search.pl \
	./scripts_temp/bp_mrtrans.pl \
	./scripts_temp/bp_mutate.pl \
	./scripts_temp/bp_nrdb.pl \
	./scripts_temp/bp_oligo_count.pl \
	./scripts_temp/bp_pairwise_kaks.pl \
	./scripts_temp/bp_pg_bulk_load_gff.pl \
	./scripts_temp/bp_process_gadfly.pl \
	./scripts_temp/bp_process_ncbi_human.pl \
	./scripts_temp/bp_process_sgd.pl \
	./scripts_temp/bp_process_wormbase.pl \
	./scripts_temp/bp_remote_blast.pl \
	./scripts_temp/bp_search2BSML.pl \
	./scripts_temp/bp_search2alnblocks.pl \
	./scripts_temp/bp_search2gff.pl \
	./scripts_temp/bp_search2tribe.pl \
	./scripts_temp/bp_search_overview.pl \
	./scripts_temp/bp_seq_length.pl \
	./scripts_temp/bp_seqconvert.pl \
	./scripts_temp/bp_split_seq.pl \
	./scripts_temp/bp_sreformat.pl \
	./scripts_temp/bp_taxid4species.pl \
	./scripts_temp/bp_translate_seq.pl
MAN3PODS = Bio/Align/AlignI.pm \
	Bio/Align/DNAStatistics.pm \
	Bio/Align/PairwiseStatistics.pm \
	Bio/Align/StatisticsI.pm \
	Bio/Align/Utilities.pm \
	Bio/AlignIO.pm \
	Bio/AlignIO/bl2seq.pm \
	Bio/AlignIO/clustalw.pm \
	Bio/AlignIO/emboss.pm \
	Bio/AlignIO/fasta.pm \
	Bio/AlignIO/maf.pm \
	Bio/AlignIO/mase.pm \
	Bio/AlignIO/mega.pm \
	Bio/AlignIO/meme.pm \
	Bio/AlignIO/metafasta.pm \
	Bio/AlignIO/msf.pm \
	Bio/AlignIO/nexus.pm \
	Bio/AlignIO/pfam.pm \
	Bio/AlignIO/phylip.pm \
	Bio/AlignIO/prodom.pm \
	Bio/AlignIO/psi.pm \
	Bio/AlignIO/selex.pm \
	Bio/AlignIO/stockholm.pm \
	Bio/AnalysisI.pm \
	Bio/AnalysisParserI.pm \
	Bio/AnalysisResultI.pm \
	Bio/AnnotatableI.pm \
	Bio/Annotation/AnnotationFactory.pm \
	Bio/Annotation/Collection.pm \
	Bio/Annotation/Comment.pm \
	Bio/Annotation/DBLink.pm \
	Bio/Annotation/OntologyTerm.pm \
	Bio/Annotation/Reference.pm \
	Bio/Annotation/SimpleValue.pm \
	Bio/Annotation/StructuredValue.pm \
	Bio/Annotation/TypeManager.pm \
	Bio/AnnotationCollectionI.pm \
	Bio/AnnotationI.pm \
	Bio/Assembly/Contig.pm \
	Bio/Assembly/ContigAnalysis.pm \
	Bio/Assembly/IO.pm \
	Bio/Assembly/IO/ace.pm \
	Bio/Assembly/IO/phrap.pm \
	Bio/Assembly/Scaffold.pm \
	Bio/Assembly/ScaffoldI.pm \
	Bio/Biblio.pm \
	Bio/Biblio/Article.pm \
	Bio/Biblio/BiblioBase.pm \
	Bio/Biblio/Book.pm \
	Bio/Biblio/BookArticle.pm \
	Bio/Biblio/IO.pm \
	Bio/Biblio/IO/medline2ref.pm \
	Bio/Biblio/IO/medlinexml.pm \
	Bio/Biblio/IO/pubmed2ref.pm \
	Bio/Biblio/IO/pubmedxml.pm \
	Bio/Biblio/Journal.pm \
	Bio/Biblio/JournalArticle.pm \
	Bio/Biblio/MedlineArticle.pm \
	Bio/Biblio/MedlineBook.pm \
	Bio/Biblio/MedlineBookArticle.pm \
	Bio/Biblio/MedlineJournal.pm \
	Bio/Biblio/MedlineJournalArticle.pm \
	Bio/Biblio/Organisation.pm \
	Bio/Biblio/Patent.pm \
	Bio/Biblio/Person.pm \
	Bio/Biblio/Proceeding.pm \
	Bio/Biblio/Provider.pm \
	Bio/Biblio/PubmedArticle.pm \
	Bio/Biblio/PubmedBookArticle.pm \
	Bio/Biblio/PubmedJournalArticle.pm \
	Bio/Biblio/Ref.pm \
	Bio/Biblio/Service.pm \
	Bio/Biblio/TechReport.pm \
	Bio/Biblio/Thesis.pm \
	Bio/Biblio/WebResource.pm \
	Bio/Cluster/ClusterFactory.pm \
	Bio/Cluster/FamilyI.pm \
	Bio/Cluster/SequenceFamily.pm \
	Bio/Cluster/UniGene.pm \
	Bio/Cluster/UniGeneI.pm \
	Bio/ClusterI.pm \
	Bio/ClusterIO.pm \
	Bio/ClusterIO/dbsnp.pm \
	Bio/ClusterIO/unigene.pm \
	Bio/CodonUsage/IO.pm \
	Bio/CodonUsage/Table.pm \
	Bio/Coordinate/Chain.pm \
	Bio/Coordinate/Collection.pm \
	Bio/Coordinate/ExtrapolatingPair.pm \
	Bio/Coordinate/GeneMapper.pm \
	Bio/Coordinate/Graph.pm \
	Bio/Coordinate/MapperI.pm \
	Bio/Coordinate/Pair.pm \
	Bio/Coordinate/Result.pm \
	Bio/Coordinate/Result/Gap.pm \
	Bio/Coordinate/Result/Match.pm \
	Bio/Coordinate/ResultI.pm \
	Bio/Coordinate/Utils.pm \
	Bio/DB/Ace.pm \
	Bio/DB/Biblio/biofetch.pm \
	Bio/DB/Biblio/soap.pm \
	Bio/DB/BiblioI.pm \
	Bio/DB/BioFetch.pm \
	Bio/DB/CUTG.pm \
	Bio/DB/DBFetch.pm \
	Bio/DB/EMBL.pm \
	Bio/DB/Failover.pm \
	Bio/DB/Fasta.pm \
	Bio/DB/FileCache.pm \
	Bio/DB/Flat.pm \
	Bio/DB/Flat/BDB.pm \
	Bio/DB/Flat/BDB/embl.pm \
	Bio/DB/Flat/BDB/fasta.pm \
	Bio/DB/Flat/BDB/genbank.pm \
	Bio/DB/Flat/BDB/swiss.pm \
	Bio/DB/Flat/BDB/swissprot.pm \
	Bio/DB/Flat/BinarySearch.pm \
	Bio/DB/GDB.pm \
	Bio/DB/GFF.pm \
	Bio/DB/GFF/Adaptor/ace.pm \
	Bio/DB/GFF/Adaptor/biofetch.pm \
	Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
	Bio/DB/GFF/Adaptor/dbi.pm \
	Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
	Bio/DB/GFF/Adaptor/dbi/iterator.pm \
	Bio/DB/GFF/Adaptor/dbi/mysql.pm \
	Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
	Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
	Bio/DB/GFF/Adaptor/dbi/oracle.pm \
	Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
	Bio/DB/GFF/Adaptor/dbi/pg.pm \
	Bio/DB/GFF/Adaptor/memory.pm \
	Bio/DB/GFF/Adaptor/memory_iterator.pm \
	Bio/DB/GFF/Aggregator.pm \
	Bio/DB/GFF/Aggregator/alignment.pm \
	Bio/DB/GFF/Aggregator/clone.pm \
	Bio/DB/GFF/Aggregator/coding.pm \
	Bio/DB/GFF/Aggregator/match.pm \
	Bio/DB/GFF/Aggregator/none.pm \
	Bio/DB/GFF/Aggregator/processed_transcript.pm \
	Bio/DB/GFF/Aggregator/transcript.pm \
	Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
	Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
	Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
	Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
	Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
	Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
	Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
	Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
	Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
	Bio/DB/GFF/Featname.pm \
	Bio/DB/GFF/Feature.pm \
	Bio/DB/GFF/Homol.pm \
	Bio/DB/GFF/RelSegment.pm \
	Bio/DB/GFF/Segment.pm \
	Bio/DB/GFF/Typename.pm \
	Bio/DB/GFF/Util/Binning.pm \
	Bio/DB/GFF/Util/Rearrange.pm \
	Bio/DB/GenBank.pm \
	Bio/DB/GenPept.pm \
	Bio/DB/InMemoryCache.pm \
	Bio/DB/MeSH.pm \
	Bio/DB/NCBIHelper.pm \
	Bio/DB/Query/GenBank.pm \
	Bio/DB/Query/WebQuery.pm \
	Bio/DB/QueryI.pm \
	Bio/DB/RandomAccessI.pm \
	Bio/DB/RefSeq.pm \
	Bio/DB/Registry.pm \
	Bio/DB/SeqI.pm \
	Bio/DB/SwissProt.pm \
	Bio/DB/Taxonomy.pm \
	Bio/DB/Taxonomy/entrez.pm \
	Bio/DB/Taxonomy/flatfile.pm \
	Bio/DB/Universal.pm \
	Bio/DB/UpdateableSeqI.pm \
	Bio/DB/WebDBSeqI.pm \
	Bio/DB/XEMBL.pm \
	Bio/DB/XEMBLService.pm \
	Bio/DBLinkContainerI.pm \
	Bio/Das/FeatureTypeI.pm \
	Bio/Das/SegmentI.pm \
	Bio/DasI.pm \
	Bio/DescribableI.pm \
	Bio/Event/EventGeneratorI.pm \
	Bio/Event/EventHandlerI.pm \
	Bio/Expression/FeatureGroup.pm \
	Bio/Expression/FeatureI.pm \
	Bio/Factory/AnalysisI.pm \
	Bio/Factory/ApplicationFactoryI.pm \
	Bio/Factory/DriverFactory.pm \
	Bio/Factory/FTLocationFactory.pm \
	Bio/Factory/HitFactoryI.pm \
	Bio/Factory/LocationFactoryI.pm \
	Bio/Factory/MapFactoryI.pm \
	Bio/Factory/ObjectBuilderI.pm \
	Bio/Factory/ObjectFactory.pm \
	Bio/Factory/ObjectFactoryI.pm \
	Bio/Factory/ResultFactoryI.pm \
	Bio/Factory/SeqAnalysisParserFactory.pm \
	Bio/Factory/SeqAnalysisParserFactoryI.pm \
	Bio/Factory/SequenceFactoryI.pm \
	Bio/Factory/SequenceProcessorI.pm \
	Bio/Factory/SequenceStreamI.pm \
	Bio/Factory/TreeFactoryI.pm \
	Bio/FeatureHolderI.pm \
	Bio/Graphics.pm \
	Bio/Graphics/Feature.pm \
	Bio/Graphics/FeatureFile.pm \
	Bio/Graphics/FeatureFile/Iterator.pm \
	Bio/Graphics/Glyph.pm \
	Bio/Graphics/Glyph/Factory.pm \
	Bio/Graphics/Glyph/alignment.pm \
	Bio/Graphics/Glyph/anchored_arrow.pm \
	Bio/Graphics/Glyph/arrow.pm \
	Bio/Graphics/Glyph/box.pm \
	Bio/Graphics/Glyph/cds.pm \
	Bio/Graphics/Glyph/crossbox.pm \
	Bio/Graphics/Glyph/diamond.pm \
	Bio/Graphics/Glyph/dna.pm \
	Bio/Graphics/Glyph/dot.pm \
	Bio/Graphics/Glyph/ellipse.pm \
	Bio/Graphics/Glyph/ex.pm \
	Bio/Graphics/Glyph/extending_arrow.pm \
	Bio/Graphics/Glyph/generic.pm \
	Bio/Graphics/Glyph/graded_segments.pm \
	Bio/Graphics/Glyph/group.pm \
	Bio/Graphics/Glyph/heterogeneous_segments.pm \
	Bio/Graphics/Glyph/line.pm \
	Bio/Graphics/Glyph/minmax.pm \
	Bio/Graphics/Glyph/oval.pm \
	Bio/Graphics/Glyph/pinsertion.pm \
	Bio/Graphics/Glyph/primers.pm \
	Bio/Graphics/Glyph/processed_transcript.pm \
	Bio/Graphics/Glyph/redgreen_box.pm \
	Bio/Graphics/Glyph/redgreen_segment.pm \
	Bio/Graphics/Glyph/rndrect.pm \
	Bio/Graphics/Glyph/ruler_arrow.pm \
	Bio/Graphics/Glyph/segmented_keyglyph.pm \
	Bio/Graphics/Glyph/segments.pm \
	Bio/Graphics/Glyph/span.pm \
	Bio/Graphics/Glyph/splice_site.pm \
	Bio/Graphics/Glyph/toomany.pm \
	Bio/Graphics/Glyph/track.pm \
	Bio/Graphics/Glyph/transcript.pm \
	Bio/Graphics/Glyph/transcript2.pm \
	Bio/Graphics/Glyph/translation.pm \
	Bio/Graphics/Glyph/triangle.pm \
	Bio/Graphics/Glyph/xyplot.pm \
	Bio/Graphics/Panel.pm \
	Bio/Graphics/Pictogram.pm \
	Bio/Graphics/RendererI.pm \
	Bio/IdCollectionI.pm \
	Bio/IdentifiableI.pm \
	Bio/Index/Abstract.pm \
	Bio/Index/AbstractSeq.pm \
	Bio/Index/Blast.pm \
	Bio/Index/EMBL.pm \
	Bio/Index/Fasta.pm \
	Bio/Index/Fastq.pm \
	Bio/Index/GenBank.pm \
	Bio/Index/SwissPfam.pm \
	Bio/Index/Swissprot.pm \
	Bio/LiveSeq/AARange.pm \
	Bio/LiveSeq/Chain.pm \
	Bio/LiveSeq/ChainI.pm \
	Bio/LiveSeq/DNA.pm \
	Bio/LiveSeq/Exon.pm \
	Bio/LiveSeq/Gene.pm \
	Bio/LiveSeq/IO/BioPerl.pm \
	Bio/LiveSeq/IO/Loader.pm \
	Bio/LiveSeq/IO/SRS.pm \
	Bio/LiveSeq/Intron.pm \
	Bio/LiveSeq/Mutation.pm \
	Bio/LiveSeq/Mutator.pm \
	Bio/LiveSeq/Prim_Transcript.pm \
	Bio/LiveSeq/Range.pm \
	Bio/LiveSeq/Repeat_Region.pm \
	Bio/LiveSeq/Repeat_Unit.pm \
	Bio/LiveSeq/SeqI.pm \
	Bio/LiveSeq/Transcript.pm \
	Bio/LiveSeq/Translation.pm \
	Bio/LocatableSeq.pm \
	Bio/Location/Atomic.pm \
	Bio/Location/AvWithinCoordPolicy.pm \
	Bio/Location/CoordinatePolicyI.pm \
	Bio/Location/Fuzzy.pm \
	Bio/Location/FuzzyLocationI.pm \
	Bio/Location/NarrowestCoordPolicy.pm \
	Bio/Location/Simple.pm \
	Bio/Location/Split.pm \
	Bio/Location/SplitLocationI.pm \
	Bio/Location/WidestCoordPolicy.pm \
	Bio/LocationI.pm \
	Bio/Map/CytoMap.pm \
	Bio/Map/CytoMarker.pm \
	Bio/Map/CytoPosition.pm \
	Bio/Map/LinkageMap.pm \
	Bio/Map/LinkagePosition.pm \
	Bio/Map/MapI.pm \
	Bio/Map/MappableI.pm \
	Bio/Map/Marker.pm \
	Bio/Map/MarkerI.pm \
	Bio/Map/Microsatellite.pm \
	Bio/Map/OrderedPosition.pm \
	Bio/Map/OrderedPositionWithDistance.pm \
	Bio/Map/Position.pm \
	Bio/Map/PositionI.pm \
	Bio/Map/SimpleMap.pm \
	Bio/MapIO.pm \
	Bio/MapIO/mapmaker.pm \
	Bio/Matrix/Generic.pm \
	Bio/Matrix/IO.pm \
	Bio/Matrix/IO/phylip.pm \
	Bio/Matrix/IO/scoring.pm \
	Bio/Matrix/MatrixI.pm \
	Bio/Matrix/PSM/IO.pm \
	Bio/Matrix/PSM/IO/mast.pm \
	Bio/Matrix/PSM/IO/meme.pm \
	Bio/Matrix/PSM/IO/transfac.pm \
	Bio/Matrix/PSM/InstanceSite.pm \
	Bio/Matrix/PSM/InstanceSiteI.pm \
	Bio/Matrix/PSM/Psm.pm \
	Bio/Matrix/PSM/PsmHeader.pm \
	Bio/Matrix/PSM/PsmHeaderI.pm \
	Bio/Matrix/PSM/PsmI.pm \
	Bio/Matrix/PSM/SiteMatrix.pm \
	Bio/Matrix/PSM/SiteMatrixI.pm \
	Bio/Matrix/PhylipDist.pm \
	Bio/Matrix/Scoring.pm \
	Bio/Ontology/GOterm.pm \
	Bio/Ontology/InterProTerm.pm \
	Bio/Ontology/Ontology.pm \
	Bio/Ontology/OntologyEngineI.pm \
	Bio/Ontology/OntologyI.pm \
	Bio/Ontology/OntologyStore.pm \
	Bio/Ontology/Path.pm \
	Bio/Ontology/PathI.pm \
	Bio/Ontology/Relationship.pm \
	Bio/Ontology/RelationshipFactory.pm \
	Bio/Ontology/RelationshipI.pm \
	Bio/Ontology/RelationshipType.pm \
	Bio/Ontology/SimpleGOEngine.pm \
	Bio/Ontology/SimpleOntologyEngine.pm \
	Bio/Ontology/Term.pm \
	Bio/Ontology/TermFactory.pm \
	Bio/Ontology/TermI.pm \
	Bio/OntologyIO.pm \
	Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
	Bio/OntologyIO/Handlers/InterProHandler.pm \
	Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm \
	Bio/OntologyIO/InterProParser.pm \
	Bio/OntologyIO/dagflat.pm \
	Bio/OntologyIO/goflat.pm \
	Bio/OntologyIO/simplehierarchy.pm \
	Bio/OntologyIO/soflat.pm \
	Bio/Perl.pm \
	Bio/Phenotype/Correlate.pm \
	Bio/Phenotype/MeSH/Term.pm \
	Bio/Phenotype/MeSH/Twig.pm \
	Bio/Phenotype/Measure.pm \
	Bio/Phenotype/OMIM/MiniMIMentry.pm \
	Bio/Phenotype/OMIM/OMIMentry.pm \
	Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm \
	Bio/Phenotype/OMIM/OMIMparser.pm \
	Bio/Phenotype/Phenotype.pm \
	Bio/Phenotype/PhenotypeI.pm \
	Bio/PopGen/Genotype.pm \
	Bio/PopGen/GenotypeI.pm \
	Bio/PopGen/IO.pm \
	Bio/PopGen/IO/csv.pm \
	Bio/PopGen/IO/prettybase.pm \
	Bio/PopGen/Individual.pm \
	Bio/PopGen/IndividualI.pm \
	Bio/PopGen/Marker.pm \
	Bio/PopGen/MarkerI.pm \
	Bio/PopGen/PopStats.pm \
	Bio/PopGen/Population.pm \
	Bio/PopGen/PopulationI.pm \
	Bio/PopGen/Simulation/Coalescent.pm \
	Bio/PopGen/Simulation/GeneticDrift.pm \
	Bio/PopGen/Statistics.pm \
	Bio/PrimarySeq.pm \
	Bio/PrimarySeqI.pm \
	Bio/Range.pm \
	Bio/RangeI.pm \
	Bio/Restriction/Analysis.pm \
	Bio/Restriction/Enzyme.pm \
	Bio/Restriction/Enzyme/MultiCut.pm \
	Bio/Restriction/Enzyme/MultiSite.pm \
	Bio/Restriction/EnzymeCollection.pm \
	Bio/Restriction/EnzymeI.pm \
	Bio/Restriction/IO.pm \
	Bio/Restriction/IO/bairoch.pm \
	Bio/Restriction/IO/base.pm \
	Bio/Restriction/IO/itype2.pm \
	Bio/Restriction/IO/withrefm.pm \
	Bio/Root/Err.pm \
	Bio/Root/Exception.pm \
	Bio/Root/Global.pm \
	Bio/Root/HTTPget.pm \
	Bio/Root/IO.pm \
	Bio/Root/IOManager.pm \
	Bio/Root/Object.pm \
	Bio/Root/Root.pm \
	Bio/Root/RootI.pm \
	Bio/Root/Storable.pm \
	Bio/Root/Utilities.pm \
	Bio/Root/Vector.pm \
	Bio/Root/Version.pm \
	Bio/Root/Xref.pm \
	Bio/Search/BlastUtils.pm \
	Bio/Search/DatabaseI.pm \
	Bio/Search/GenericDatabase.pm \
	Bio/Search/HSP/BlastHSP.pm \
	Bio/Search/HSP/FastaHSP.pm \
	Bio/Search/HSP/GenericHSP.pm \
	Bio/Search/HSP/HMMERHSP.pm \
	Bio/Search/HSP/HSPFactory.pm \
	Bio/Search/HSP/HSPI.pm \
	Bio/Search/HSP/PSLHSP.pm \
	Bio/Search/HSP/PsiBlastHSP.pm \
	Bio/Search/HSP/WABAHSP.pm \
	Bio/Search/Hit/BlastHit.pm \
	Bio/Search/Hit/Fasta.pm \
	Bio/Search/Hit/GenericHit.pm \
	Bio/Search/Hit/HMMERHit.pm \
	Bio/Search/Hit/HitFactory.pm \
	Bio/Search/Hit/HitI.pm \
	Bio/Search/Hit/PsiBlastHit.pm \
	Bio/Search/Iteration/GenericIteration.pm \
	Bio/Search/Iteration/IterationI.pm \
	Bio/Search/Processor.pm \
	Bio/Search/Result/BlastResult.pm \
	Bio/Search/Result/GenericResult.pm \
	Bio/Search/Result/HMMERResult.pm \
	Bio/Search/Result/ResultFactory.pm \
	Bio/Search/Result/ResultI.pm \
	Bio/Search/Result/WABAResult.pm \
	Bio/Search/SearchUtils.pm \
	Bio/SearchDist.pm \
	Bio/SearchIO.pm \
	Bio/SearchIO/EventHandlerI.pm \
	Bio/SearchIO/FastHitEventBuilder.pm \
	Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
	Bio/SearchIO/SearchResultEventBuilder.pm \
	Bio/SearchIO/SearchWriterI.pm \
	Bio/SearchIO/Writer/BSMLResultWriter.pm \
	Bio/SearchIO/Writer/GbrowseGFF.pm \
	Bio/SearchIO/Writer/HSPTableWriter.pm \
	Bio/SearchIO/Writer/HTMLResultWriter.pm \
	Bio/SearchIO/Writer/HitTableWriter.pm \
	Bio/SearchIO/Writer/ResultTableWriter.pm \
	Bio/SearchIO/Writer/TextResultWriter.pm \
	Bio/SearchIO/axt.pm \
	Bio/SearchIO/blast.pm \
	Bio/SearchIO/blasttable.pm \
	Bio/SearchIO/blastxml.pm \
	Bio/SearchIO/exonerate.pm \
	Bio/SearchIO/fasta.pm \
	Bio/SearchIO/hmmer.pm \
	Bio/SearchIO/megablast.pm \
	Bio/SearchIO/psl.pm \
	Bio/SearchIO/sim4.pm \
	Bio/SearchIO/waba.pm \
	Bio/SearchIO/wise.pm \
	Bio/Seq.pm \
	Bio/Seq/BaseSeqProcessor.pm \
	Bio/Seq/EncodedSeq.pm \
	Bio/Seq/LargePrimarySeq.pm \
	Bio/Seq/LargeSeq.pm \
	Bio/Seq/Meta.pm \
	Bio/Seq/Meta/Array.pm \
	Bio/Seq/MetaI.pm \
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	Bio/Seq/PrimedSeq.pm \
	Bio/Seq/QualI.pm \
	Bio/Seq/RichSeq.pm \
	Bio/Seq/RichSeqI.pm \
	Bio/Seq/SeqBuilder.pm \
	Bio/Seq/SeqFactory.pm \
	Bio/Seq/SeqFastaSpeedFactory.pm \
	Bio/Seq/SeqWithQuality.pm \
	Bio/Seq/SequenceTrace.pm \
	Bio/Seq/TraceI.pm \
	Bio/SeqAnalysisParserI.pm \
	Bio/SeqFeature/AnnotationAdaptor.pm \
	Bio/SeqFeature/Collection.pm \
	Bio/SeqFeature/CollectionI.pm \
	Bio/SeqFeature/Computation.pm \
	Bio/SeqFeature/FeaturePair.pm \
	Bio/SeqFeature/Gene/Exon.pm \
	Bio/SeqFeature/Gene/ExonI.pm \
	Bio/SeqFeature/Gene/GeneStructure.pm \
	Bio/SeqFeature/Gene/GeneStructureI.pm \
	Bio/SeqFeature/Gene/Intron.pm \
	Bio/SeqFeature/Gene/NC_Feature.pm \
	Bio/SeqFeature/Gene/Poly_A_site.pm \
	Bio/SeqFeature/Gene/Promoter.pm \
	Bio/SeqFeature/Gene/Transcript.pm \
	Bio/SeqFeature/Gene/TranscriptI.pm \
	Bio/SeqFeature/Gene/UTR.pm \
	Bio/SeqFeature/Generic.pm \
	Bio/SeqFeature/PositionProxy.pm \
	Bio/SeqFeature/Primer.pm \
	Bio/SeqFeature/SiRNA/Oligo.pm \
	Bio/SeqFeature/SiRNA/Pair.pm \
	Bio/SeqFeature/Similarity.pm \
	Bio/SeqFeature/SimilarityPair.pm \
	Bio/SeqFeature/Tools/TypeMapper.pm \
	Bio/SeqFeature/Tools/Unflattener.pm \
	Bio/SeqFeatureI.pm \
	Bio/SeqI.pm \
	Bio/SeqIO.pm \
	Bio/SeqIO/FTHelper.pm \
	Bio/SeqIO/MultiFile.pm \
	Bio/SeqIO/abi.pm \
	Bio/SeqIO/ace.pm \
	Bio/SeqIO/alf.pm \
	Bio/SeqIO/asciitree.pm \
	Bio/SeqIO/bsml.pm \
	Bio/SeqIO/chadoxml.pm \
	Bio/SeqIO/ctf.pm \
	Bio/SeqIO/embl.pm \
	Bio/SeqIO/exp.pm \
	Bio/SeqIO/fasta.pm \
	Bio/SeqIO/fastq.pm \
	Bio/SeqIO/game.pm \
	Bio/SeqIO/game/featHandler.pm \
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	Bio/SeqIO/game/gameSubs.pm \
	Bio/SeqIO/game/gameWriter.pm \
	Bio/SeqIO/game/seqHandler.pm \
	Bio/SeqIO/gcg.pm \
	Bio/SeqIO/genbank.pm \
	Bio/SeqIO/kegg.pm \
	Bio/SeqIO/largefasta.pm \
	Bio/SeqIO/locuslink.pm \
	Bio/SeqIO/metafasta.pm \
	Bio/SeqIO/phd.pm \
	Bio/SeqIO/pir.pm \
	Bio/SeqIO/pln.pm \
	Bio/SeqIO/qual.pm \
	Bio/SeqIO/raw.pm \
	Bio/SeqIO/scf.pm \
	Bio/SeqIO/swiss.pm \
	Bio/SeqIO/tab.pm \
	Bio/SeqIO/tigr.pm \
	Bio/SeqIO/ztr.pm \
	Bio/SeqUtils.pm \
	Bio/SimpleAlign.pm \
	Bio/SimpleAnalysisI.pm \
	Bio/Species.pm \
	Bio/Structure/Atom.pm \
	Bio/Structure/Chain.pm \
	Bio/Structure/Entry.pm \
	Bio/Structure/IO.pm \
	Bio/Structure/IO/pdb.pm \
	Bio/Structure/Model.pm \
	Bio/Structure/Residue.pm \
	Bio/Structure/SecStr/DSSP/Res.pm \
	Bio/Structure/SecStr/STRIDE/Res.pm \
	Bio/Structure/StructureI.pm \
	Bio/Symbol/Alphabet.pm \
	Bio/Symbol/AlphabetI.pm \
	Bio/Symbol/DNAAlphabet.pm \
	Bio/Symbol/ProteinAlphabet.pm \
	Bio/Symbol/Symbol.pm \
	Bio/Symbol/SymbolI.pm \
	Bio/Taxonomy.pm \
	Bio/Taxonomy/FactoryI.pm \
	Bio/Taxonomy/Node.pm \
	Bio/Taxonomy/Taxon.pm \
	Bio/Taxonomy/Tree.pm \
	Bio/Tools/AlignFactory.pm \
	Bio/Tools/Alignment/Consed.pm \
	Bio/Tools/Alignment/Trim.pm \
	Bio/Tools/Analysis/DNA/ESEfinder.pm \
	Bio/Tools/Analysis/Protein/Domcut.pm \
	Bio/Tools/Analysis/Protein/ELM.pm \
	Bio/Tools/Analysis/Protein/GOR4.pm \
	Bio/Tools/Analysis/Protein/HNN.pm \
	Bio/Tools/Analysis/Protein/Mitoprot.pm \
	Bio/Tools/Analysis/Protein/NetPhos.pm \
	Bio/Tools/Analysis/Protein/Scansite.pm \
	Bio/Tools/Analysis/Protein/Sopma.pm \
	Bio/Tools/Analysis/SimpleAnalysisBase.pm \
	Bio/Tools/AnalysisResult.pm \
	Bio/Tools/BPbl2seq.pm \
	Bio/Tools/BPlite.pm \
	Bio/Tools/BPlite/HSP.pm \
	Bio/Tools/BPlite/Iteration.pm \
	Bio/Tools/BPlite/Sbjct.pm \
	Bio/Tools/BPpsilite.pm \
	Bio/Tools/Blast.pm \
	Bio/Tools/Blast/HSP.pm \
	Bio/Tools/Blast/HTML.pm \
	Bio/Tools/Blast/Sbjct.pm \
	Bio/Tools/Blat.pm \
	Bio/Tools/CodonTable.pm \
	Bio/Tools/Coil.pm \
	Bio/Tools/ECnumber.pm \
	Bio/Tools/EMBOSS/Palindrome.pm \
	Bio/Tools/EPCR.pm \
	Bio/Tools/ESTScan.pm \
	Bio/Tools/Eponine.pm \
	Bio/Tools/Est2Genome.pm \
	Bio/Tools/FootPrinter.pm \
	Bio/Tools/GFF.pm \
	Bio/Tools/Gel.pm \
	Bio/Tools/Geneid.pm \
	Bio/Tools/Genemark.pm \
	Bio/Tools/Genewise.pm \
	Bio/Tools/Genomewise.pm \
	Bio/Tools/Genscan.pm \
	Bio/Tools/Glimmer.pm \
	Bio/Tools/Grail.pm \
	Bio/Tools/GuessSeqFormat.pm \
	Bio/Tools/HMMER/Domain.pm \
	Bio/Tools/HMMER/Results.pm \
	Bio/Tools/HMMER/Set.pm \
	Bio/Tools/Hmmpfam.pm \
	Bio/Tools/IUPAC.pm \
	Bio/Tools/Lucy.pm \
	Bio/Tools/MZEF.pm \
	Bio/Tools/OddCodes.pm \
	Bio/Tools/Phylo/Molphy.pm \
	Bio/Tools/Phylo/Molphy/Result.pm \
	Bio/Tools/Phylo/PAML.pm \
	Bio/Tools/Phylo/PAML/ModelResult.pm \
	Bio/Tools/Phylo/PAML/Result.pm \
	Bio/Tools/Phylo/Phylip/ProtDist.pm \
	Bio/Tools/Prediction/Exon.pm \
	Bio/Tools/Prediction/Gene.pm \
	Bio/Tools/Primer/Assessor/Base.pm \
	Bio/Tools/Primer/AssessorI.pm \
	Bio/Tools/Primer/Feature.pm \
	Bio/Tools/Primer/Pair.pm \
	Bio/Tools/Primer3.pm \
	Bio/Tools/Prints.pm \
	Bio/Tools/Profile.pm \
	Bio/Tools/Promoterwise.pm \
	Bio/Tools/PrositeScan.pm \
	Bio/Tools/Pseudowise.pm \
	Bio/Tools/QRNA.pm \
	Bio/Tools/RandomDistFunctions.pm \
	Bio/Tools/RepeatMasker.pm \
	Bio/Tools/RestrictionEnzyme.pm \
	Bio/Tools/Run/RemoteBlast.pm \
	Bio/Tools/Run/StandAloneBlast.pm \
	Bio/Tools/Run/WrapperBase.pm \
	Bio/Tools/Seg.pm \
	Bio/Tools/SeqAnal.pm \
	Bio/Tools/SeqPattern.pm \
	Bio/Tools/SeqStats.pm \
	Bio/Tools/SeqWords.pm \
	Bio/Tools/SiRNA.pm \
	Bio/Tools/Sigcleave.pm \
	Bio/Tools/Signalp.pm \
	Bio/Tools/Sim4/Exon.pm \
	Bio/Tools/Sim4/Results.pm \
	Bio/Tools/Tmhmm.pm \
	Bio/Tools/WWW.pm \
	Bio/Tools/dpAlign.pm \
	Bio/Tools/pICalculator.pm \
	Bio/Tools/pSW.pm \
	Bio/Tree/AlleleNode.pm \
	Bio/Tree/Node.pm \
	Bio/Tree/NodeI.pm \
	Bio/Tree/NodeNHX.pm \
	Bio/Tree/RandomFactory.pm \
	Bio/Tree/Statistics.pm \
	Bio/Tree/Tree.pm \
	Bio/Tree/TreeFunctionsI.pm \
	Bio/Tree/TreeI.pm \
	Bio/TreeIO.pm \
	Bio/TreeIO/TreeEventBuilder.pm \
	Bio/TreeIO/lintree.pm \
	Bio/TreeIO/newick.pm \
	Bio/TreeIO/nexus.pm \
	Bio/TreeIO/nhx.pm \
	Bio/TreeIO/svggraph.pm \
	Bio/TreeIO/tabtree.pm \
	Bio/UpdateableSeqI.pm \
	Bio/Variation/AAChange.pm \
	Bio/Variation/AAReverseMutate.pm \
	Bio/Variation/Allele.pm \
	Bio/Variation/DNAMutation.pm \
	Bio/Variation/IO.pm \
	Bio/Variation/IO/flat.pm \
	Bio/Variation/IO/xml.pm \
	Bio/Variation/RNAChange.pm \
	Bio/Variation/SNP.pm \
	Bio/Variation/SeqDiff.pm \
	Bio/Variation/VariantI.pm \
	Bio/WebAgent.pm \
	biodatabases.pod \
	biodesign.pod \
	bioperl.pod \
	bioscripts.pod \
	bptutorial.pl
HTMLEXT = html
INST_MAN1DIR = blib/man1
INSTALLMAN1DIR = /usr/share/doclib/annex/man/man1
MAN1EXT = 1
INST_MAN3DIR = blib/man3
INSTALLMAN3DIR = /usr/share/doclib/annex/man/man3
MAN3EXT = 3
PERM_RW = 644
PERM_RWX = 755

# work around a famous dec-osf make(1) feature(?):
makemakerdflt: all

.SUFFIXES: .xs .c .C .cpp .cxx .cc $(OBJ_EXT)

# Nick wanted to get rid of .PRECIOUS. I don't remember why. I seem to recall, that
# some make implementations will delete the Makefile when we rebuild it. Because
# we call false(1) when we rebuild it. So make(1) is not completely wrong when it
# does so. Our milage may vary.
# .PRECIOUS: Makefile    # seems to be not necessary anymore

.PHONY: all config static dynamic test linkext manifest

# Where is the Config information that we are using/depend on
CONFIGDEP = $(PERL_ARCHLIB)/Config.pm $(PERL_INC)/config.h

# Where to put 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    =

EXPORT_LIST = 

PERL_ARCHIVE = 

TO_INST_PM = Bio/Align/AlignI.pm \
	Bio/Align/DNAStatistics.pm \
	Bio/Align/PairwiseStatistics.pm \
	Bio/Align/StatisticsI.pm \
	Bio/Align/Utilities.pm \
	Bio/AlignIO.pm \
	Bio/AlignIO/bl2seq.pm \
	Bio/AlignIO/clustalw.pm \
	Bio/AlignIO/emboss.pm \
	Bio/AlignIO/fasta.pm \
	Bio/AlignIO/maf.pm \
	Bio/AlignIO/mase.pm \
	Bio/AlignIO/mega.pm \
	Bio/AlignIO/meme.pm \
	Bio/AlignIO/metafasta.pm \
	Bio/AlignIO/msf.pm \
	Bio/AlignIO/nexus.pm \
	Bio/AlignIO/pfam.pm \
	Bio/AlignIO/phylip.pm \
	Bio/AlignIO/prodom.pm \
	Bio/AlignIO/psi.pm \
	Bio/AlignIO/selex.pm \
	Bio/AlignIO/stockholm.pm \
	Bio/AnalysisI.pm \
	Bio/AnalysisParserI.pm \
	Bio/AnalysisResultI.pm \
	Bio/AnnotatableI.pm \
	Bio/Annotation/AnnotationFactory.pm \
	Bio/Annotation/Collection.pm \
	Bio/Annotation/Comment.pm \
	Bio/Annotation/DBLink.pm \
	Bio/Annotation/OntologyTerm.pm \
	Bio/Annotation/Reference.pm \
	Bio/Annotation/SimpleValue.pm \
	Bio/Annotation/StructuredValue.pm \
	Bio/Annotation/TypeManager.pm \
	Bio/AnnotationCollectionI.pm \
	Bio/AnnotationI.pm \
	Bio/Assembly/Contig.pm \
	Bio/Assembly/ContigAnalysis.pm \
	Bio/Assembly/IO.pm \
	Bio/Assembly/IO/ace.pm \
	Bio/Assembly/IO/phrap.pm \
	Bio/Assembly/Scaffold.pm \
	Bio/Assembly/ScaffoldI.pm \
	Bio/Biblio.pm \
	Bio/Biblio/Article.pm \
	Bio/Biblio/BiblioBase.pm \
	Bio/Biblio/Book.pm \
	Bio/Biblio/BookArticle.pm \
	Bio/Biblio/IO.pm \
	Bio/Biblio/IO/medline2ref.pm \
	Bio/Biblio/IO/medlinexml.pm \
	Bio/Biblio/IO/pubmed2ref.pm \
	Bio/Biblio/IO/pubmedxml.pm \
	Bio/Biblio/Journal.pm \
	Bio/Biblio/JournalArticle.pm \
	Bio/Biblio/MedlineArticle.pm \
	Bio/Biblio/MedlineBook.pm \
	Bio/Biblio/MedlineBookArticle.pm \
	Bio/Biblio/MedlineJournal.pm \
	Bio/Biblio/MedlineJournalArticle.pm \
	Bio/Biblio/Organisation.pm \
	Bio/Biblio/Patent.pm \
	Bio/Biblio/Person.pm \
	Bio/Biblio/Proceeding.pm \
	Bio/Biblio/Provider.pm \
	Bio/Biblio/PubmedArticle.pm \
	Bio/Biblio/PubmedBookArticle.pm \
	Bio/Biblio/PubmedJournalArticle.pm \
	Bio/Biblio/Ref.pm \
	Bio/Biblio/Service.pm \
	Bio/Biblio/TechReport.pm \
	Bio/Biblio/Thesis.pm \
	Bio/Biblio/WebResource.pm \
	Bio/Cluster/ClusterFactory.pm \
	Bio/Cluster/FamilyI.pm \
	Bio/Cluster/SequenceFamily.pm \
	Bio/Cluster/UniGene.pm \
	Bio/Cluster/UniGeneI.pm \
	Bio/ClusterI.pm \
	Bio/ClusterIO.pm \
	Bio/ClusterIO/dbsnp.pm \
	Bio/ClusterIO/unigene.pm \
	Bio/CodonUsage/IO.pm \
	Bio/CodonUsage/Table.pm \
	Bio/Coordinate/Chain.pm \
	Bio/Coordinate/Collection.pm \
	Bio/Coordinate/ExtrapolatingPair.pm \
	Bio/Coordinate/GeneMapper.pm \
	Bio/Coordinate/Graph.pm \
	Bio/Coordinate/MapperI.pm \
	Bio/Coordinate/Pair.pm \
	Bio/Coordinate/Result.pm \
	Bio/Coordinate/Result/Gap.pm \
	Bio/Coordinate/Result/Match.pm \
	Bio/Coordinate/ResultI.pm \
	Bio/Coordinate/Utils.pm \
	Bio/DB/Ace.pm \
	Bio/DB/Biblio/biofetch.pm \
	Bio/DB/Biblio/soap.pm \
	Bio/DB/BiblioI.pm \
	Bio/DB/BioFetch.pm \
	Bio/DB/CUTG.pm \
	Bio/DB/DBFetch.pm \
	Bio/DB/EMBL.pm \
	Bio/DB/Failover.pm \
	Bio/DB/Fasta.pm \
	Bio/DB/FileCache.pm \
	Bio/DB/Flat.pm \
	Bio/DB/Flat/BDB.pm \
	Bio/DB/Flat/BDB/embl.pm \
	Bio/DB/Flat/BDB/fasta.pm \
	Bio/DB/Flat/BDB/genbank.pm \
	Bio/DB/Flat/BDB/swiss.pm \
	Bio/DB/Flat/BDB/swissprot.pm \
	Bio/DB/Flat/BinarySearch.pm \
	Bio/DB/GDB.pm \
	Bio/DB/GFF.pm \
	Bio/DB/GFF/Adaptor/ace.pm \
	Bio/DB/GFF/Adaptor/biofetch.pm \
	Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
	Bio/DB/GFF/Adaptor/dbi.pm \
	Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
	Bio/DB/GFF/Adaptor/dbi/iterator.pm \
	Bio/DB/GFF/Adaptor/dbi/mysql.pm \
	Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
	Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
	Bio/DB/GFF/Adaptor/dbi/oracle.pm \
	Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
	Bio/DB/GFF/Adaptor/dbi/pg.pm \
	Bio/DB/GFF/Adaptor/memory.pm \
	Bio/DB/GFF/Adaptor/memory_iterator.pm \
	Bio/DB/GFF/Aggregator.pm \
	Bio/DB/GFF/Aggregator/alignment.pm \
	Bio/DB/GFF/Aggregator/clone.pm \
	Bio/DB/GFF/Aggregator/coding.pm \
	Bio/DB/GFF/Aggregator/match.pm \
	Bio/DB/GFF/Aggregator/none.pm \
	Bio/DB/GFF/Aggregator/processed_transcript.pm \
	Bio/DB/GFF/Aggregator/transcript.pm \
	Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
	Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
	Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
	Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
	Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
	Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
	Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
	Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
	Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
	Bio/DB/GFF/Featname.pm \
	Bio/DB/GFF/Feature.pm \
	Bio/DB/GFF/Homol.pm \
	Bio/DB/GFF/RelSegment.pm \
	Bio/DB/GFF/Segment.pm \
	Bio/DB/GFF/Typename.pm \
	Bio/DB/GFF/Util/Binning.pm \
	Bio/DB/GFF/Util/Rearrange.pm \
	Bio/DB/GenBank.pm \
	Bio/DB/GenPept.pm \
	Bio/DB/InMemoryCache.pm \
	Bio/DB/MANIFEST \
	Bio/DB/Makefile.PL \
	Bio/DB/MeSH.pm \
	Bio/DB/NCBIHelper.pm \
	Bio/DB/Query/GenBank.pm \
	Bio/DB/Query/WebQuery.pm \
	Bio/DB/QueryI.pm \
	Bio/DB/RandomAccessI.pm \
	Bio/DB/RefSeq.pm \
	Bio/DB/Registry.pm \
	Bio/DB/SeqI.pm \
	Bio/DB/SwissProt.pm \
	Bio/DB/Taxonomy.pm \
	Bio/DB/Taxonomy/entrez.pm \
	Bio/DB/Taxonomy/flatfile.pm \
	Bio/DB/Universal.pm \
	Bio/DB/UpdateableSeqI.pm \
	Bio/DB/WebDBSeqI.pm \
	Bio/DB/XEMBL.pm \
	Bio/DB/XEMBLService.pm \
	Bio/DBLinkContainerI.pm \
	Bio/Das/FeatureTypeI.pm \
	Bio/Das/SegmentI.pm \
	Bio/DasI.pm \
	Bio/DescribableI.pm \
	Bio/Event/EventGeneratorI.pm \
	Bio/Event/EventHandlerI.pm \
	Bio/Expression/FeatureGroup.pm \
	Bio/Expression/FeatureGroup/FeatureGroupMas50.pm \
	Bio/Expression/FeatureI.pm \
	Bio/Expression/FeatureSet/FeatureSetMas50.pm \
	Bio/Factory/AnalysisI.pm \
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	-@$(CHMOD) $(PERM_RWX) $(INST_AUTODIR)

$(INST_LIBDIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
	@$(MKPATH) $(INST_LIBDIR)
	@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_LIBDIR)/.exists

	-@$(CHMOD) $(PERM_RWX) $(INST_LIBDIR)

$(INST_ARCHAUTODIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
	@$(MKPATH) $(INST_ARCHAUTODIR)
	@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_ARCHAUTODIR)/.exists

	-@$(CHMOD) $(PERM_RWX) $(INST_ARCHAUTODIR)

config :: $(INST_MAN1DIR)/.exists
	@$(NOOP)


$(INST_MAN1DIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
	@$(MKPATH) $(INST_MAN1DIR)
	@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_MAN1DIR)/.exists

	-@$(CHMOD) $(PERM_RWX) $(INST_MAN1DIR)

config :: $(INST_MAN3DIR)/.exists
	@$(NOOP)


$(INST_MAN3DIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
	@$(MKPATH) $(INST_MAN3DIR)
	@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_MAN3DIR)/.exists

	-@$(CHMOD) $(PERM_RWX) $(INST_MAN3DIR)

help:
	perldoc ExtUtils::MakeMaker

Version_check:
	@$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) \
		-MExtUtils::MakeMaker=Version_check \
		-e "Version_check('$(MM_VERSION)')"


# --- MakeMaker linkext section:

linkext :: $(LINKTYPE)
	@$(NOOP)


# --- MakeMaker dlsyms section:


# --- MakeMaker dynamic section:

## $(INST_PM) has been moved to the all: target.
## It remains here for awhile to allow for old usage: "make dynamic"
#dynamic :: Makefile $(INST_DYNAMIC) $(INST_BOOT) $(INST_PM)
dynamic :: Makefile $(INST_DYNAMIC) $(INST_BOOT)
	@$(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 :: Makefile $(INST_STATIC) $(INST_PM)
static :: Makefile $(INST_STATIC)
	@$(NOOP)


# --- MakeMaker static_lib section:


# --- MakeMaker htmlifypods section:

htmlifypods : pure_all
	@$(NOOP)


# --- MakeMaker manifypods section:

manifypods : pure_all
	@$(NOOP)


# --- MakeMaker processPL section:

all :: bioscripts.pod
	@$(NOOP)

bioscripts.pod :: doc/makedoc.PL
	$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL bioscripts.pod

all :: biodatabases.pod
	@$(NOOP)

biodatabases.pod :: doc/makedoc.PL
	$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL biodatabases.pod

all :: biodesign.pod
	@$(NOOP)

biodesign.pod :: doc/makedoc.PL
	$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL biodesign.pod

all :: bioperl.pod
	@$(NOOP)

bioperl.pod :: doc/makedoc.PL
	$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL bioperl.pod


# --- MakeMaker installbin section:

$(INST_SCRIPT)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
	@$(MKPATH) $(INST_SCRIPT)
	@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_SCRIPT)/.exists

	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)

EXE_FILES = ./scripts_temp/bp_load_gff.pl ./scripts_temp/bp_genbank2gff.pl ./scripts_temp/bp_bulk_load_gff.pl ./scripts_temp/bp_fast_load_gff.pl ./scripts_temp/bp_generate_histogram.pl ./scripts_temp/bp_pg_bulk_load_gff.pl ./scripts_temp/bp_process_gadfly.pl ./scripts_temp/bp_process_ncbi_human.pl ./scripts_temp/bp_process_sgd.pl ./scripts_temp/bp_process_wormbase.pl ./scripts_temp/bp_biofetch_genbank_proxy.pl ./scripts_temp/bp_bioflat_index.pl ./scripts_temp/bp_biogetseq.pl ./scripts_temp/bp_flanks.pl ./scripts_temp/bp_biblio.pl ./scripts_temp/bp_frend.pl ./scripts_temp/bp_feature_draw.pl ./scripts_temp/bp_search_overview.pl ./scripts_temp/bp_fetch.pl ./scripts_temp/bp_index.pl ./scripts_temp/bp_composite_LD.pl ./scripts_temp/bp_heterogeneity_test.pl ./scripts_temp/bp_filter_search.pl ./scripts_temp/bp_extract_feature_seq.pl ./scripts_temp/bp_seqconvert.pl ./scripts_temp/bp_split_seq.pl ./scripts_temp/bp_translate_seq.pl ./scripts_temp/bp_aacomp.pl ./scripts_temp/bp_chaos_plot.pl ./scripts_temp/bp_gccalc.pl ./scripts_temp/bp_oligo_count.pl ./scripts_temp/bp_local_taxonomydb_query.pl ./scripts_temp/bp_taxid4species.pl ./scripts_temp/bp_blast2tree.pl ./scripts_temp/bp_nrdb.pl ./scripts_temp/bp_mrtrans.pl ./scripts_temp/bp_sreformat.pl ./scripts_temp/bp_dbsplit.pl ./scripts_temp/bp_mask_by_search.pl ./scripts_temp/bp_mutate.pl ./scripts_temp/bp_pairwise_kaks.pl ./scripts_temp/bp_remote_blast.pl ./scripts_temp/bp_search2BSML.pl ./scripts_temp/bp_search2alnblocks.pl ./scripts_temp/bp_search2gff.pl ./scripts_temp/bp_search2tribe.pl ./scripts_temp/bp_seq_length.pl

FIXIN = $(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::MakeMaker \
    -e "MY->fixin(shift)"

pure_all :: $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_sreformat.pl $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_biogetseq.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_index.pl $(INST_SCRIPT)/bp_split_seq.pl $(INST_SCRIPT)/bp_remote_blast.pl $(INST_SCRIPT)/bp_aacomp.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_frend.pl $(INST_SCRIPT)/bp_generate_histogram.pl $(INST_SCRIPT)/bp_process_sgd.pl $(INST_SCRIPT)/bp_mutate.pl $(INST_SCRIPT)/bp_filter_search.pl $(INST_SCRIPT)/bp_genbank2gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_nrdb.pl $(INST_SCRIPT)/bp_blast2tree.pl
	@$(NOOP)

realclean ::
	rm -f $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_sreformat.pl $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_biogetseq.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_index.pl $(INST_SCRIPT)/bp_split_seq.pl $(INST_SCRIPT)/bp_remote_blast.pl $(INST_SCRIPT)/bp_aacomp.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_frend.pl $(INST_SCRIPT)/bp_generate_histogram.pl $(INST_SCRIPT)/bp_process_sgd.pl $(INST_SCRIPT)/bp_mutate.pl $(INST_SCRIPT)/bp_filter_search.pl $(INST_SCRIPT)/bp_genbank2gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_nrdb.pl $(INST_SCRIPT)/bp_blast2tree.pl

$(INST_SCRIPT)/bp_chaos_plot.pl: ./scripts_temp/bp_chaos_plot.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_chaos_plot.pl
	cp ./scripts_temp/bp_chaos_plot.pl $(INST_SCRIPT)/bp_chaos_plot.pl
	$(FIXIN) $(INST_SCRIPT)/bp_chaos_plot.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_chaos_plot.pl

$(INST_SCRIPT)/bp_composite_LD.pl: ./scripts_temp/bp_composite_LD.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_composite_LD.pl
	cp ./scripts_temp/bp_composite_LD.pl $(INST_SCRIPT)/bp_composite_LD.pl
	$(FIXIN) $(INST_SCRIPT)/bp_composite_LD.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_composite_LD.pl

$(INST_SCRIPT)/bp_pairwise_kaks.pl: ./scripts_temp/bp_pairwise_kaks.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_pairwise_kaks.pl
	cp ./scripts_temp/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl
	$(FIXIN) $(INST_SCRIPT)/bp_pairwise_kaks.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_pairwise_kaks.pl

$(INST_SCRIPT)/bp_flanks.pl: ./scripts_temp/bp_flanks.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_flanks.pl
	cp ./scripts_temp/bp_flanks.pl $(INST_SCRIPT)/bp_flanks.pl
	$(FIXIN) $(INST_SCRIPT)/bp_flanks.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_flanks.pl

$(INST_SCRIPT)/bp_translate_seq.pl: ./scripts_temp/bp_translate_seq.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_translate_seq.pl
	cp ./scripts_temp/bp_translate_seq.pl $(INST_SCRIPT)/bp_translate_seq.pl
	$(FIXIN) $(INST_SCRIPT)/bp_translate_seq.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_translate_seq.pl

$(INST_SCRIPT)/bp_feature_draw.pl: ./scripts_temp/bp_feature_draw.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_feature_draw.pl
	cp ./scripts_temp/bp_feature_draw.pl $(INST_SCRIPT)/bp_feature_draw.pl
	$(FIXIN) $(INST_SCRIPT)/bp_feature_draw.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_feature_draw.pl

$(INST_SCRIPT)/bp_load_gff.pl: ./scripts_temp/bp_load_gff.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_load_gff.pl
	cp ./scripts_temp/bp_load_gff.pl $(INST_SCRIPT)/bp_load_gff.pl
	$(FIXIN) $(INST_SCRIPT)/bp_load_gff.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_load_gff.pl

$(INST_SCRIPT)/bp_biblio.pl: ./scripts_temp/bp_biblio.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_biblio.pl
	cp ./scripts_temp/bp_biblio.pl $(INST_SCRIPT)/bp_biblio.pl
	$(FIXIN) $(INST_SCRIPT)/bp_biblio.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biblio.pl

$(INST_SCRIPT)/bp_fast_load_gff.pl: ./scripts_temp/bp_fast_load_gff.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_fast_load_gff.pl
	cp ./scripts_temp/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_fast_load_gff.pl
	$(FIXIN) $(INST_SCRIPT)/bp_fast_load_gff.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_fast_load_gff.pl

$(INST_SCRIPT)/bp_search_overview.pl: ./scripts_temp/bp_search_overview.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_search_overview.pl
	cp ./scripts_temp/bp_search_overview.pl $(INST_SCRIPT)/bp_search_overview.pl
	$(FIXIN) $(INST_SCRIPT)/bp_search_overview.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search_overview.pl

$(INST_SCRIPT)/bp_search2tribe.pl: ./scripts_temp/bp_search2tribe.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_search2tribe.pl
	cp ./scripts_temp/bp_search2tribe.pl $(INST_SCRIPT)/bp_search2tribe.pl
	$(FIXIN) $(INST_SCRIPT)/bp_search2tribe.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2tribe.pl

$(INST_SCRIPT)/bp_fetch.pl: ./scripts_temp/bp_fetch.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_fetch.pl
	cp ./scripts_temp/bp_fetch.pl $(INST_SCRIPT)/bp_fetch.pl
	$(FIXIN) $(INST_SCRIPT)/bp_fetch.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_fetch.pl

$(INST_SCRIPT)/bp_seq_length.pl: ./scripts_temp/bp_seq_length.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_seq_length.pl
	cp ./scripts_temp/bp_seq_length.pl $(INST_SCRIPT)/bp_seq_length.pl
	$(FIXIN) $(INST_SCRIPT)/bp_seq_length.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_seq_length.pl

$(INST_SCRIPT)/bp_search2gff.pl: ./scripts_temp/bp_search2gff.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_search2gff.pl
	cp ./scripts_temp/bp_search2gff.pl $(INST_SCRIPT)/bp_search2gff.pl
	$(FIXIN) $(INST_SCRIPT)/bp_search2gff.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2gff.pl

$(INST_SCRIPT)/bp_extract_feature_seq.pl: ./scripts_temp/bp_extract_feature_seq.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_extract_feature_seq.pl
	cp ./scripts_temp/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl
	$(FIXIN) $(INST_SCRIPT)/bp_extract_feature_seq.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_extract_feature_seq.pl

$(INST_SCRIPT)/bp_pg_bulk_load_gff.pl: ./scripts_temp/bp_pg_bulk_load_gff.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
	cp ./scripts_temp/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
	$(FIXIN) $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl

$(INST_SCRIPT)/bp_sreformat.pl: ./scripts_temp/bp_sreformat.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_sreformat.pl
	cp ./scripts_temp/bp_sreformat.pl $(INST_SCRIPT)/bp_sreformat.pl
	$(FIXIN) $(INST_SCRIPT)/bp_sreformat.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_sreformat.pl

$(INST_SCRIPT)/bp_dbsplit.pl: ./scripts_temp/bp_dbsplit.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_dbsplit.pl
	cp ./scripts_temp/bp_dbsplit.pl $(INST_SCRIPT)/bp_dbsplit.pl
	$(FIXIN) $(INST_SCRIPT)/bp_dbsplit.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_dbsplit.pl

$(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl: ./scripts_temp/bp_biofetch_genbank_proxy.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
	cp ./scripts_temp/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
	$(FIXIN) $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl

$(INST_SCRIPT)/bp_bioflat_index.pl: ./scripts_temp/bp_bioflat_index.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_bioflat_index.pl
	cp ./scripts_temp/bp_bioflat_index.pl $(INST_SCRIPT)/bp_bioflat_index.pl
	$(FIXIN) $(INST_SCRIPT)/bp_bioflat_index.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_bioflat_index.pl

$(INST_SCRIPT)/bp_search2alnblocks.pl: ./scripts_temp/bp_search2alnblocks.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_search2alnblocks.pl
	cp ./scripts_temp/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_search2alnblocks.pl
	$(FIXIN) $(INST_SCRIPT)/bp_search2alnblocks.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2alnblocks.pl

$(INST_SCRIPT)/bp_local_taxonomydb_query.pl: ./scripts_temp/bp_local_taxonomydb_query.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
	cp ./scripts_temp/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
	$(FIXIN) $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_local_taxonomydb_query.pl

$(INST_SCRIPT)/bp_biogetseq.pl: ./scripts_temp/bp_biogetseq.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_biogetseq.pl
	cp ./scripts_temp/bp_biogetseq.pl $(INST_SCRIPT)/bp_biogetseq.pl
	$(FIXIN) $(INST_SCRIPT)/bp_biogetseq.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biogetseq.pl

$(INST_SCRIPT)/bp_process_wormbase.pl: ./scripts_temp/bp_process_wormbase.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_process_wormbase.pl
	cp ./scripts_temp/bp_process_wormbase.pl $(INST_SCRIPT)/bp_process_wormbase.pl
	$(FIXIN) $(INST_SCRIPT)/bp_process_wormbase.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_wormbase.pl

$(INST_SCRIPT)/bp_search2BSML.pl: ./scripts_temp/bp_search2BSML.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_search2BSML.pl
	cp ./scripts_temp/bp_search2BSML.pl $(INST_SCRIPT)/bp_search2BSML.pl
	$(FIXIN) $(INST_SCRIPT)/bp_search2BSML.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2BSML.pl

$(INST_SCRIPT)/bp_taxid4species.pl: ./scripts_temp/bp_taxid4species.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_taxid4species.pl
	cp ./scripts_temp/bp_taxid4species.pl $(INST_SCRIPT)/bp_taxid4species.pl
	$(FIXIN) $(INST_SCRIPT)/bp_taxid4species.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_taxid4species.pl

$(INST_SCRIPT)/bp_mask_by_search.pl: ./scripts_temp/bp_mask_by_search.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_mask_by_search.pl
	cp ./scripts_temp/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mask_by_search.pl
	$(FIXIN) $(INST_SCRIPT)/bp_mask_by_search.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mask_by_search.pl

$(INST_SCRIPT)/bp_mrtrans.pl: ./scripts_temp/bp_mrtrans.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_mrtrans.pl
	cp ./scripts_temp/bp_mrtrans.pl $(INST_SCRIPT)/bp_mrtrans.pl
	$(FIXIN) $(INST_SCRIPT)/bp_mrtrans.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mrtrans.pl

$(INST_SCRIPT)/bp_process_gadfly.pl: ./scripts_temp/bp_process_gadfly.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_process_gadfly.pl
	cp ./scripts_temp/bp_process_gadfly.pl $(INST_SCRIPT)/bp_process_gadfly.pl
	$(FIXIN) $(INST_SCRIPT)/bp_process_gadfly.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_gadfly.pl

$(INST_SCRIPT)/bp_gccalc.pl: ./scripts_temp/bp_gccalc.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_gccalc.pl
	cp ./scripts_temp/bp_gccalc.pl $(INST_SCRIPT)/bp_gccalc.pl
	$(FIXIN) $(INST_SCRIPT)/bp_gccalc.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_gccalc.pl

$(INST_SCRIPT)/bp_seqconvert.pl: ./scripts_temp/bp_seqconvert.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_seqconvert.pl
	cp ./scripts_temp/bp_seqconvert.pl $(INST_SCRIPT)/bp_seqconvert.pl
	$(FIXIN) $(INST_SCRIPT)/bp_seqconvert.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_seqconvert.pl

$(INST_SCRIPT)/bp_oligo_count.pl: ./scripts_temp/bp_oligo_count.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_oligo_count.pl
	cp ./scripts_temp/bp_oligo_count.pl $(INST_SCRIPT)/bp_oligo_count.pl
	$(FIXIN) $(INST_SCRIPT)/bp_oligo_count.pl
	-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_oligo_count.pl

$(INST_SCRIPT)/bp_process_ncbi_human.pl: ./scripts_temp/bp_process_ncbi_human.pl Makefile $(INST_SCRIPT)/.exists
	@rm -f $(INST_SCRIPT)/bp_process_ncbi_human.pl
	cp ./scripts_temp/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl
	$(FIXIN) $(INST_SCRIPT)/bp_process_ncbi_human.pl
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$(INST_SCRIPT)/bp_generate_histogram.pl: ./scripts_temp/bp_generate_histogram.pl Makefile $(INST_SCRIPT)/.exists
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$(INST_SCRIPT)/bp_process_sgd.pl: ./scripts_temp/bp_process_sgd.pl Makefile $(INST_SCRIPT)/.exists
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$(INST_SCRIPT)/bp_mutate.pl: ./scripts_temp/bp_mutate.pl Makefile $(INST_SCRIPT)/.exists
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# --- MakeMaker subdirs section:

# none

# --- MakeMaker clean section:

# Delete temporary files but do not touch installed files. We don't delete
# the Makefile here so a later make realclean still has a makefile to use.

clean ::
	-rm -rf ./blib $(MAKE_APERL_FILE) $(INST_ARCHAUTODIR)/extralibs.all perlmain.c mon.out core core.*perl.*.? *perl.core so_locations pm_to_blib *~ */*~ */*/*~ *$(OBJ_EXT) *$(LIB_EXT) perl.exe $(BOOTSTRAP) $(BASEEXT).bso $(BASEEXT).def $(BASEEXT).exp
	-mv Makefile Makefile.old $(DEV_NULL)
	-rm -rf scripts_temp


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uninstall :: uninstall_from_$(INSTALLDIRS)dirs

uninstall_from_perldirs ::
	@$(UNINSTALL) $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist

uninstall_from_sitedirs ::
	@$(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist


# --- MakeMaker force section:
# Phony target to force checking subdirectories.
FORCE:
	@$(NOOP)


# --- MakeMaker perldepend section:


# --- MakeMaker makefile section:

# We take a very conservative approach here, but it\'s worth it.
# We move Makefile to Makefile.old here to avoid gnu make looping.
Makefile : Makefile.PL $(CONFIGDEP)
	@echo "Makefile out-of-date with respect to $?"
	@echo "Cleaning current config before rebuilding Makefile..."
	-@$(RM_F) Makefile.old
	-@$(MV) Makefile Makefile.old
	-$(MAKE) -f Makefile.old clean $(DEV_NULL) || $(NOOP)
	$(PERL) "-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" Makefile.PL 
	@echo "==> Your Makefile has been rebuilt. <=="
	@echo "==> Please rerun the make command.  <=="
	false

# To change behavior to :: would be nice, but would break Tk b9.02
# so you find such a warning below the dist target.
#Makefile :: $(VERSION_FROM)
#	@echo "Warning: Makefile possibly out of date with $(VERSION_FROM)"


# --- MakeMaker staticmake section:

# --- MakeMaker makeaperl section ---
MAP_TARGET    = perl
FULLPERL      = /usr/bin/perl

$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
	$(MAKE) -f $(MAKE_APERL_FILE) $@

$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE)
	@echo Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
	@$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) \
		Makefile.PL DIR= \
		MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
		MAKEAPERL=1 NORECURS=1 CCCDLFLAGS=


# --- MakeMaker test section:

TEST_VERBOSE=0
TEST_TYPE=test_$(LINKTYPE)
TEST_FILE = test.pl
TEST_FILES = 
TESTDB_SW = -d

testdb :: testdb_$(LINKTYPE)

test :: $(TEST_TYPE)
	@echo 'No tests defined for $(NAME) extension.'

test_dynamic :: pure_all

testdb_dynamic :: pure_all
	PERL_DL_NONLAZY=1 $(FULLPERL) $(TESTDB_SW) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) $(TEST_FILE)

test_ : test_dynamic

test_static :: test_dynamic
testdb_static :: testdb_dynamic


# --- MakeMaker ppd section:
# Creates a PPD (Perl Package Description) for a binary distribution.
ppd:
	@$(PERL) -e "print qq{<SOFTPKG NAME=\"bioperl\" VERSION=\"1,4,0,0\">\n}. qq{\t<TITLE>bioperl</TITLE>\n}. qq{\t<ABSTRACT>Bioinformatics Toolkit</ABSTRACT>\n}. qq{\t<AUTHOR>Bioperl Team (bioperl-l\@bioperl.org)</AUTHOR>\n}. qq{\t<IMPLEMENTATION>\n}. qq{\t\t<DEPENDENCY NAME=\"DB_File\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"File-Spec\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"File-Temp\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"HTML-Entities\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"IO-Scalar\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"IO-String\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<OS NAME=\"$(OSNAME)\" />\n}. qq{\t\t<ARCHITECTURE NAME=\"alpha-dec_osf\" />\n}. qq{\t\t<CODEBASE HREF=\"\" />\n}. qq{\t</IMPLEMENTATION>\n}. qq{</SOFTPKG>\n}" > bioperl.ppd

# --- MakeMaker pm_to_blib section:

pm_to_blib: $(TO_INST_PM)
	@$(PERL) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" \
	"-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" -MExtUtils::Install \
        -e "pm_to_blib({qw{$(PM_TO_BLIB)}},'$(INST_LIB)/auto')"
	@$(TOUCH) $@


# --- MakeMaker selfdocument section:


# --- MakeMaker postamble section:
show_tests :
	@echo 'type make test_<subtest> to run'
	@echo ''





# End.
-------------- next part --------------



-------------------------------
  Dr. Wolf-Gerolf THIES        
  ITG - Tox, Bau 439, Zi 507   
  Forschungszentrum Karlsruhe  
  Postfach 3640                
  D-76021 Karlsruhe            
  Tel: +49 7247 82-3139/-3547  
  Fax: +49 7247 82 3557        
  E-mail: thies at itg.fzk.de     
--------------------------------


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