From ef5a1dd75966652741df15fde349496dcaa8efaf Mon Sep 17 00:00:00 2001 From: jtb Date: Thu, 5 Apr 2001 21:48:40 +0000 Subject: Updated to bioperl-0.7.0. Revision history for Bioperl core modules 0.7 Large number of changes, including refactoring of the Object system, new parsers, new functionality and all round better system. Highlights are: o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI; Bio::Root::IO for I/O and file/handle capabilities. o Imported BPlite modules from Ian Korf for BLAST parsing. This is considered the supported BLAST parser; Bio::Tools::Blast.pm will eventually phase out due to lack of support. o Improved Sequence Feature model. Added complete location modelling (with fuzzy and compound locations). See Bio::LocationI and the modules under Bio/Location. Added support in Genbank/EMBL format parsing to completely parse feature tables for complex locations. o Moved special support for databanks etc to specialized modules under Bio/Seq/. One of these supports very large sequences through a temporary file as a backend. o Explicit Gene, Transcript and Exon SeqFeature objects, supporting CDS retrieval and exon shuffling. o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and DB/GDB (the latter has platform-specific limitations). o New analysis parser framework for HT sequence annotation (see Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory) o New Alignment IO framework o New Index modules (Swissprot) o New modules for running Blast within perl (Bio::Tools::Run::StandAloneBlast). Added modules for running Multiple Sequence Alignment tools ClustalW and TCoffee (Bio::Tools::Run::Alignment). o New Cookbook-style tutorial (see bptutorial.pl). Improved documentation across the package. o Much improved cross platform support. Many known incompatibilities have been fixed; however, NT and Mac do not work across the entire setup (see PLATFORMS). o Many bug fixes, code restructuring, etc. Overall stability and maintainability benefit a lot. o A total of 957 automatic tests 0.6.2 There are very few functionality changes but a large number of software improvements/bug fixes across the package. o The EMBL/GenBank parsing are improved. o The Swissprot reading is improved. Swissprot writing is disabled as it doesn't work at all. This needs to wait for 0.7 release o BLAST reports with no hits are correctly parsed. o Several other bugs of the BLAST parser (regular expressions, ...) fixed. o Old syntax calls have been replaced with more modern syntax o Modules that did not work at all, in particular the Sim4 set have been removed o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair have improved compliance with interface specs and documentation o Mailing list documentation updated throughout the distribution o Most minor bug fixes have happened. o The scripts in /examples now work and have the modern syntax rather than the deprecated syntax 0.6.1 Sun April 2 2000 o Sequences can have Sequence Features attached to them - The sequence features can be read from or written to EMBL and GenBank style flat files o Objects for Annotation, including References (but not full medline abstracts), Database links and Comments are provided o A Species object to represent nodes on a taxonomy tree is provided o The ability to parse HMMER and Sim4 output has been added o The Blast parsing has been improved, with better PSI-BLAST support and better overall behaviour. o Flat file indexed databases provide both random access and sequential access to their component sequences. o A CodonTable object has been written with all known CodonTables accessible. o A number of new lightweight analysis tools have been added, such as molecular weight determination. The 0.6 release also has improved software engineering o The sequence objects have been rewritten, providing more maintainable and easier to implement objects. These objects are backwardly compatible with the 0.05.1 objects o Many objects are defined in terms of interfaces and then a Perl implementation has been provided. The interfaces are found in the 'I' files (module names ending in 'I'). This means that it is possible to wrap C/CORBA/SQL access as true "bioperl" objects, compatible with the rest of bioperl. o The SeqIO system has been overhauled to provide better processing and perl-like automatic interpretation of <> over arguments. o Many more tests have been added (a total of 172 automatic tests are now run before release). 0.05.1 Tue Jun 29 05:30:44 1999 - Central distribution now requires Perl 5.004. This was done to get around 5.003-based problems in Bio/Index/* and SimpleAlign. - Various bug fixes in the Bio::Tools::Blast modules including better exception handling and PSI-Blast support. See Bio/Tools/Blast/CHANGES for more. - Fixed the Parse mechanism in Seq.pm to use readseq. Follow the instructions in README for how to install it (basically, you have to edit Parse.pm). - Improved documentation of Seq.pm, indicating where objects are returned and where strings are returned. - Fixed uninitialized warnings in Bio::Root::Object.pm and Bio::Tools::SeqPattern.pm. - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52. 0.05 Sun Apr 25 01:14:11 1999 - Bio::Tools::Blast modules have less memory problems and faster parsing. Webblast uses LWP and supports more functionality. See Bio/Tools/Blast/CHANGES for more. - The Bio::SeqIO system has been started, moving the sequence reformatting code out of the sequence object - The Bio::Index:: system has been started, providing generic index capabilities and specifically works for Fasta formatted databases and EMBL .dat formatted databases - The Bio::DB:: system started, providing access to databases, both via flat file + index (see above) and via http to NCBI - The scripts/ directory, where industrial strength scripts are put has been started. - Many changes - a better distribution all round. --- biology/bioperl/Makefile | 21 ++++------------- biology/bioperl/files/md5 | 4 ++-- biology/bioperl/files/patch-sum | 9 ++++---- biology/bioperl/patches/patch-aa | 16 ------------- biology/bioperl/patches/patch-ab | 20 ---------------- biology/bioperl/patches/patch-ac | 13 ----------- biology/bioperl/pkg/PLIST | 50 ++++++++++++++++++++++------------------ 7 files changed, 40 insertions(+), 93 deletions(-) delete mode 100644 biology/bioperl/patches/patch-aa delete mode 100644 biology/bioperl/patches/patch-ab delete mode 100644 biology/bioperl/patches/patch-ac (limited to 'biology/bioperl') diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile index 1b46c91af2c..fcea148fbb7 100644 --- a/biology/bioperl/Makefile +++ b/biology/bioperl/Makefile @@ -1,32 +1,21 @@ -# $NetBSD: Makefile,v 1.3 2001/02/16 13:41:26 wiz Exp $ +# $NetBSD: Makefile,v 1.4 2001/04/05 21:48:40 jtb Exp $ # -DISTNAME= bioperl-0.04.4 +DISTNAME= bioperl-0.7.0 CATEGORIES= biology -MASTER_SITES= ftp://bio.perl.org/pub/DIST/ +MASTER_SITES= http://bioperl.org/Core/Latest/ MAINTAINER= packages@netbsd.org -HOMEPAGE= http://bio.perl.org/ +HOMEPAGE= http://bioperl.org/ COMMENT= Perl tools for computational molecular biology USE_PERL5= # defined PERL5_PACKLIST= ${PERL5_SITEARCH}/auto/Bio/.packlist -PERL5_PACKLIST+= ${PERL5_SITEARCH}/auto/bp_sw/.packlist do-configure: - cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL - cd ${WRKSRC}/Compile/SW; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL - -pre-build: - cd ${WRKSRC}/Compile/SW/libs; ${MAKE_PROGRAM} - -post-build: - cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} - cd ${WRKSRC}; ${MAKE_PROGRAM} test - cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} test + @cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL post-install: - cd ${WRKSRC}/Compile/SW; ${MAKE_PROGRAM} install ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/bioperl cd ${WRKSRC}/examples; ${GTAR} cf - . \ | (cd ${PREFIX}/share/examples/bioperl; ${GTAR} xf -) diff --git a/biology/bioperl/files/md5 b/biology/bioperl/files/md5 index 41efd041385..d97ecad284c 100644 --- a/biology/bioperl/files/md5 +++ b/biology/bioperl/files/md5 @@ -1,3 +1,3 @@ -$NetBSD: md5,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ +$NetBSD: md5,v 1.2 2001/04/05 21:48:40 jtb Exp $ -MD5 (bioperl-0.04.4.tar.gz) = e131dfd837423ec0fc746a3b83e68020 +SHA1 (bioperl-0.7.0.tar.gz) = c86abeeb5f2e2b98d1577d9cefd51ce15bbcb6b6 diff --git a/biology/bioperl/files/patch-sum b/biology/bioperl/files/patch-sum index 1cfc5723524..24b54b7806f 100644 --- a/biology/bioperl/files/patch-sum +++ b/biology/bioperl/files/patch-sum @@ -1,5 +1,6 @@ -$NetBSD: patch-sum,v 1.2 2000/08/26 03:36:38 jlam Exp $ +$NetBSD: patch-sum,v 1.3 2001/04/05 21:48:40 jtb Exp $ -MD5 (patch-aa) = c18e708c55eeae44ac7ec7a860d67f00 -MD5 (patch-ab) = cf3fd5491b9aac607ed516ce4cf0213c -MD5 (patch-ac) = 4de5755319b2d54ce180633847275c92 +This placeholder file is generated by the ``makepatchsum'' target +whenever the patches directory is empty or missing. Its purpose +is to ensure that the presence of any obsolete patches will cause +the proper error to be emitted at build time. diff --git a/biology/bioperl/patches/patch-aa b/biology/bioperl/patches/patch-aa deleted file mode 100644 index 704b8fdc216..00000000000 --- a/biology/bioperl/patches/patch-aa +++ /dev/null @@ -1,16 +0,0 @@ -$NetBSD: patch-aa,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ - ---- Compile/SW/Makefile.PL.orig Fri Dec 11 08:24:25 1998 -+++ Compile/SW/Makefile.PL Mon Mar 1 11:37:15 1999 -@@ -13,9 +13,9 @@ - - sub MY::postamble{ - ' --$(MYEXTLIB): libs/libsw$(LIB_EXT) -+$(MYEXTLIB): - DEFINE=\'$(DEFINE)\'; CC=\'$(PERLMAINCC)\'; export DEFINE INC CC; \ -- cd libs && $(MAKE) libsw.a -e -+ cd libs && $(MAKE) libsw$(LIB_EXT) -e - - '; - } diff --git a/biology/bioperl/patches/patch-ab b/biology/bioperl/patches/patch-ab deleted file mode 100644 index b76fbbaa9b0..00000000000 --- a/biology/bioperl/patches/patch-ab +++ /dev/null @@ -1,20 +0,0 @@ -$NetBSD: patch-ab,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ - ---- Compile/SW/libs/makefile.orig Fri Dec 11 16:24:29 1998 -+++ Compile/SW/libs/makefile Sat Apr 10 21:45:14 1999 -@@ -1,5 +1,4 @@ -- -- -+CFLAGS+=-fPIC - - OBJS = aln.o\ - alnconvert.o\ -@@ -52,7 +51,5 @@ - ar ru libsw.a $(OBJS) - - wisefile.o : wisefile.c -- $(CC) $(CFLAGS) -DNOERROR wisefile.c -+ ${CC} ${CFLAGS} -c -DNOERROR wisefile.c - --CFLAGS = -c -O --CC = cc diff --git a/biology/bioperl/patches/patch-ac b/biology/bioperl/patches/patch-ac deleted file mode 100644 index 064961c8ae6..00000000000 --- a/biology/bioperl/patches/patch-ac +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-ac,v 1.1 2000/08/26 03:36:45 jlam Exp $ - ---- Bio/Root/Err.pm.orig Thu Feb 4 03:06:35 1999 -+++ Bio/Root/Err.pm -@@ -984,7 +984,7 @@ - : This method is an alternative to Bio::Root::Object::throw() - : and is not as well developed or documented as that method. - --See Also : L(), B, B(), B, B - - =cut - diff --git a/biology/bioperl/pkg/PLIST b/biology/bioperl/pkg/PLIST index 4e429081653..99571fe9ec6 100644 --- a/biology/bioperl/pkg/PLIST +++ b/biology/bioperl/pkg/PLIST @@ -1,9 +1,4 @@ -@comment $NetBSD: PLIST,v 1.2 2000/08/27 07:10:59 jlam Exp $ -share/examples/bioperl/blast/blast_config.pl -share/examples/bioperl/blast/blast_seq.pl -share/examples/bioperl/blast/example.table1 -share/examples/bioperl/blast/example.table2 -share/examples/bioperl/blast/html.pl +@comment $NetBSD: PLIST,v 1.3 2001/04/05 21:48:41 jtb Exp $ share/examples/bioperl/blast/out/blastn.2.gz share/examples/bioperl/blast/out/blastn.2.wu.gz share/examples/bioperl/blast/out/blastp.1.gcg.gz @@ -19,26 +14,44 @@ share/examples/bioperl/blast/out/blastx.2 share/examples/bioperl/blast/out/blastx.2.email.gz share/examples/bioperl/blast/out/blastx.208.gz share/examples/bioperl/blast/out/tblastn.206.out.gz -share/examples/bioperl/blast/parse.pl -share/examples/bioperl/blast/parse2.pl -share/examples/bioperl/blast/parse_multi.pl -share/examples/bioperl/blast/parse_positions.pl -share/examples/bioperl/blast/parse_stream.pl -share/examples/bioperl/blast/print_blasts.pl -share/examples/bioperl/blast/run.pl share/examples/bioperl/blast/seq/acc1.dna.fasta share/examples/bioperl/blast/seq/seqs.fasta share/examples/bioperl/blast/seq/yal011w.dna.fasta share/examples/bioperl/blast/seq/yel009c.fasta share/examples/bioperl/blast/seq/ymr284w.fasta +share/examples/bioperl/blast/blast_config.pl +share/examples/bioperl/blast/blast_seq.pl +share/examples/bioperl/blast/example.table1 +share/examples/bioperl/blast/example.table2 +share/examples/bioperl/blast/html.pl +share/examples/bioperl/blast/parse_blast.pl +share/examples/bioperl/blast/parse_blast2.pl +share/examples/bioperl/blast/parse_multi.pl +share/examples/bioperl/blast/parse_positions.pl +share/examples/bioperl/blast/print_blasts.pl +share/examples/bioperl/blast/retrieve_blast.pl +share/examples/bioperl/blast/run_blast_remote.pl share/examples/bioperl/blosum62.bla +share/examples/bioperl/change_gene.pl +share/examples/bioperl/clustalw.pl +share/examples/bioperl/getGenBank.pl share/examples/bioperl/gon250.bla +share/examples/bioperl/gsequence +share/examples/bioperl/hitdisplay.pl share/examples/bioperl/psw.pl share/examples/bioperl/restriction.pl share/examples/bioperl/rev_and_trans.pl +share/examples/bioperl/seq_pattern.pl +share/examples/bioperl/simplealign.pl +share/examples/bioperl/standaloneblast.pl +share/examples/bioperl/test-genscan.pl +share/examples/bioperl/root_object/Outer.pm share/examples/bioperl/root_object/Bar.pm share/examples/bioperl/root_object/Foo.pm -share/examples/bioperl/root_object/Outer.pm +share/examples/bioperl/root_object/vector/Person.pm +share/examples/bioperl/root_object/vector/PersonManager.pm +share/examples/bioperl/root_object/vector/vector.out +share/examples/bioperl/root_object/vector/vector.pl share/examples/bioperl/root_object/destroy.pl share/examples/bioperl/root_object/error.out share/examples/bioperl/root_object/error.pl @@ -51,21 +64,14 @@ share/examples/bioperl/root_object/read.test share/examples/bioperl/root_object/read.test2 share/examples/bioperl/root_object/read.test3 share/examples/bioperl/root_object/utilities.pl -share/examples/bioperl/root_object/vector/Person.pm -share/examples/bioperl/root_object/vector/PersonManager.pm -share/examples/bioperl/root_object/vector/vector.out -share/examples/bioperl/root_object/vector/vector.pl -share/examples/bioperl/seq/id.list share/examples/bioperl/seq/seq.fasta.gz +share/examples/bioperl/seq/id.list share/examples/bioperl/seq/seq1.fasta share/examples/bioperl/seq/seq2.fasta share/examples/bioperl/seq/seqs1.pl share/examples/bioperl/seq/seqs2.pl share/examples/bioperl/seq/seqs3.pl -share/examples/bioperl/seq/seqs4.pl share/examples/bioperl/seq/seqtools.pl -share/examples/bioperl/seq_pattern.pl -share/examples/bioperl/simplealign.pl @dirrm share/examples/bioperl/seq @dirrm share/examples/bioperl/root_object/vector @dirrm share/examples/bioperl/root_object -- cgit v1.2.3