From 4f01d3ffa1bea1d5ee733d966bed920032212170 Mon Sep 17 00:00:00 2001 From: rh Date: Fri, 16 Apr 1999 14:43:35 +0000 Subject: Initial import of bioperl-0.04.4, based on the collection of packages submitted in PR pkg/7075 by Brook Milligan, with several modifications. --- biology/bioperl/Makefile | 31 +++++++++ biology/bioperl/README.html | 65 ++++++++++++++++++ biology/bioperl/files/md5 | 3 + biology/bioperl/patches/patch-aa | 16 +++++ biology/bioperl/patches/patch-ab | 20 ++++++ biology/bioperl/pkg/COMMENT | 1 + biology/bioperl/pkg/DESCR | 11 +++ biology/bioperl/pkg/PLIST | 141 +++++++++++++++++++++++++++++++++++++++ 8 files changed, 288 insertions(+) create mode 100644 biology/bioperl/Makefile create mode 100644 biology/bioperl/README.html create mode 100644 biology/bioperl/files/md5 create mode 100644 biology/bioperl/patches/patch-aa create mode 100644 biology/bioperl/patches/patch-ab create mode 100644 biology/bioperl/pkg/COMMENT create mode 100644 biology/bioperl/pkg/DESCR create mode 100644 biology/bioperl/pkg/PLIST (limited to 'biology/bioperl') diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile new file mode 100644 index 00000000000..1e40805a8c5 --- /dev/null +++ b/biology/bioperl/Makefile @@ -0,0 +1,31 @@ +# $NetBSD: Makefile,v 1.1.1.1 1999/04/16 14:43:35 rh Exp $ +# + +DISTNAME= bioperl-0.04.4 +CATEGORIES= biology +MASTER_SITES= ftp://bio.perl.org/pub/DIST/ + +MAINTAINER= packages@netbsd.org +HOMEPAGE= http://bio.perl.org/ + +USE_PERL5= yes + +do-configure: + cd ${WRKSRC}; perl Makefile.PL + cd ${WRKSRC}/Compile/SW; perl Makefile.PL + +pre-build: + cd ${WRKSRC}/Compile/SW/libs; make + +post-build: + cd ${WRKSRC}/Compile/SW; make + cd ${WRKSRC}; make test + cd ${WRKSRC}/Compile/SW; make test + +post-install: + cd ${WRKSRC}/Compile/SW; make install + ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/bioperl + cd ${WRKSRC}/examples; ${GTAR} cf - . \ + | (cd ${PREFIX}/share/examples/bioperl; ${GTAR} xf -) + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/bioperl/README.html b/biology/bioperl/README.html new file mode 100644 index 00000000000..32955ae338f --- /dev/null +++ b/biology/bioperl/README.html @@ -0,0 +1,65 @@ + + + +The NetBSD Packages Collection: biology/bioperl + + + + +

+ +

The NetBSD Packages Collection: biology/bioperl

+ +

Brief description of the package:
+ +Perl tools for computational molecular biology + +

+ +

Please read the file "pkg/DESCR" for a +longer description. +

+ +

This package has a home page at http://bio.perl.org/.

+ + + +

The package is located in the +"biology/bioperl" +directory. It can be manipulated using the packaging tools, +working on the +bioperl-0.04.4 +package. +For a summary on how to use the package collection, go to the +top of the packages tree. +

+ + +

+This package requires the following package(s) to build: +perl-5.00404 +. +

+This package requires the following package(s) to run: +perl-5.00404 +. +

+ +

+Click here to download the package in +precompiled binary form for the following machine architectures: +

(no precompiled binaries available)

+ +

+[ + Go up one level +| + Go to top of packages tree +] + + diff --git a/biology/bioperl/files/md5 b/biology/bioperl/files/md5 new file mode 100644 index 00000000000..41efd041385 --- /dev/null +++ b/biology/bioperl/files/md5 @@ -0,0 +1,3 @@ +$NetBSD: md5,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ + +MD5 (bioperl-0.04.4.tar.gz) = e131dfd837423ec0fc746a3b83e68020 diff --git a/biology/bioperl/patches/patch-aa b/biology/bioperl/patches/patch-aa new file mode 100644 index 00000000000..704b8fdc216 --- /dev/null +++ b/biology/bioperl/patches/patch-aa @@ -0,0 +1,16 @@ +$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 new file mode 100644 index 00000000000..b76fbbaa9b0 --- /dev/null +++ b/biology/bioperl/patches/patch-ab @@ -0,0 +1,20 @@ +$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/pkg/COMMENT b/biology/bioperl/pkg/COMMENT new file mode 100644 index 00000000000..dcecfcecbdb --- /dev/null +++ b/biology/bioperl/pkg/COMMENT @@ -0,0 +1 @@ +Perl tools for computational molecular biology diff --git a/biology/bioperl/pkg/DESCR b/biology/bioperl/pkg/DESCR new file mode 100644 index 00000000000..8c86b48648d --- /dev/null +++ b/biology/bioperl/pkg/DESCR @@ -0,0 +1,11 @@ + The Bioperl project is a coordinated effort to collect computational +methods routinely used in bioinformatics into a set of standard +CPAN-style, well-documented, and freely available Perl modules. Perl +provides unparalleled support for many tasks common in bioinformatics +yet there are no standard Perl modules for biology. Bioperl hopes to +help fill this void. + + Bioperl modules and source code will always be freely available +under the same terms as Perl itself. The Bioperl project is open to +all and we invite suggestions and participation from the larger +bioinformatics community. diff --git a/biology/bioperl/pkg/PLIST b/biology/bioperl/pkg/PLIST new file mode 100644 index 00000000000..c9fe1f000db --- /dev/null +++ b/biology/bioperl/pkg/PLIST @@ -0,0 +1,141 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 1999/04/16 14:43:36 rh Exp $ +lib/perl5/man/man3/Bio::Parse.3 +lib/perl5/man/man3/Bio::Root::Err.3 +lib/perl5/man/man3/Bio::Root::IOManager.3 +lib/perl5/man/man3/Bio::Root::Object.3 +lib/perl5/man/man3/Bio::Root::Utilities.3 +lib/perl5/man/man3/Bio::Root::Vector.3 +lib/perl5/man/man3/Bio::Root::Xref.3 +lib/perl5/man/man3/Bio::Seq.3 +lib/perl5/man/man3/Bio::SimpleAlign.3 +lib/perl5/man/man3/Bio::Tools::AlignFactory.3 +lib/perl5/man/man3/Bio::Tools::Blast.3 +lib/perl5/man/man3/Bio::Tools::Blast::HSP.3 +lib/perl5/man/man3/Bio::Tools::Blast::HTML.3 +lib/perl5/man/man3/Bio::Tools::Blast::Run::LocalBlast.3 +lib/perl5/man/man3/Bio::Tools::Blast::Run::Webblast.3 +lib/perl5/man/man3/Bio::Tools::Blast::Sbjct.3 +lib/perl5/man/man3/Bio::Tools::Fasta.3 +lib/perl5/man/man3/Bio::Tools::RestrictionEnzyme.3 +lib/perl5/man/man3/Bio::Tools::SeqAnal.3 +lib/perl5/man/man3/Bio::Tools::SeqPattern.3 +lib/perl5/man/man3/Bio::Tools::WWW.3 +lib/perl5/man/man3/Bio::Tools::pSW.3 +lib/perl5/man/man3/Bio::UnivAln.3 +lib/perl5/man/man3/bioperl.3 +lib/perl5/site_perl/Bio/Parse.pm +lib/perl5/site_perl/Bio/Root/Err.pm +lib/perl5/site_perl/Bio/Root/Global.pm +lib/perl5/site_perl/Bio/Root/IOManager.pm +lib/perl5/site_perl/Bio/Root/Object.pm +lib/perl5/site_perl/Bio/Root/Utilities.pm +lib/perl5/site_perl/Bio/Root/Vector.pm +lib/perl5/site_perl/Bio/Root/Xref.pm +lib/perl5/site_perl/Bio/Seq.pm +lib/perl5/site_perl/Bio/SimpleAlign.pm +lib/perl5/site_perl/Bio/Tools/AlignFactory.pm +lib/perl5/site_perl/Bio/Tools/Blast.pm +lib/perl5/site_perl/Bio/Tools/Blast/CHANGES +lib/perl5/site_perl/Bio/Tools/Blast/HSP.pm +lib/perl5/site_perl/Bio/Tools/Blast/HTML.pm +lib/perl5/site_perl/Bio/Tools/Blast/Run/LocalBlast.pm +lib/perl5/site_perl/Bio/Tools/Blast/Run/Makefile.PL +lib/perl5/site_perl/Bio/Tools/Blast/Run/Webblast.pm +lib/perl5/site_perl/Bio/Tools/Blast/Run/postclient.pl +lib/perl5/site_perl/Bio/Tools/Blast/Sbjct.pm +lib/perl5/site_perl/Bio/Tools/Fasta.pm +lib/perl5/site_perl/Bio/Tools/RestrictionEnzyme.pm +lib/perl5/site_perl/Bio/Tools/SeqAnal.pm +lib/perl5/site_perl/Bio/Tools/SeqPattern.pm +lib/perl5/site_perl/Bio/Tools/WWW.pm +lib/perl5/site_perl/Bio/Tools/pSW.pm +lib/perl5/site_perl/Bio/UnivAln.pm +lib/perl5/site_perl/auto/bp_sw/autosplit.ix +lib/perl5/site_perl/bioperl.pod +lib/perl5/site_perl/bp_sw.pm +lib/perl5/site_perl/${MACHINE_ARCH}-netbsd/auto/Bio/.packlist +lib/perl5/site_perl/${MACHINE_ARCH}-netbsd/auto/bp_sw/.packlist +lib/perl5/site_perl/${MACHINE_ARCH}-netbsd/auto/bp_sw/bp_sw.bs +lib/perl5/site_perl/${MACHINE_ARCH}-netbsd/auto/bp_sw/bp_sw.so +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/out/blastn.2.gz +share/examples/bioperl/blast/out/blastn.2.wu.gz +share/examples/bioperl/blast/out/blastp.1.gcg.gz +share/examples/bioperl/blast/out/blastp.1.gz +share/examples/bioperl/blast/out/blastp.2.gz +share/examples/bioperl/blast/out/blastp.2.nogap.gz +share/examples/bioperl/blast/out/blastp.2.wu +share/examples/bioperl/blast/out/blastp.205.gz +share/examples/bioperl/blast/out/blastp.2a.gz +share/examples/bioperl/blast/out/blastp.2b.gz +share/examples/bioperl/blast/out/blastp.email.html.gz +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/blosum62.bla +share/examples/bioperl/gon250.bla +share/examples/bioperl/psw.pl +share/examples/bioperl/restriction.pl +share/examples/bioperl/rev_and_trans.pl +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/destroy.pl +share/examples/bioperl/root_object/error.out +share/examples/bioperl/root_object/error.pl +share/examples/bioperl/root_object/filehandle.out +share/examples/bioperl/root_object/filehandle.pl +share/examples/bioperl/root_object/io.out +share/examples/bioperl/root_object/io.pl +share/examples/bioperl/root_object/read.pl +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/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 +@dirrm share/examples/bioperl/blast/seq +@dirrm share/examples/bioperl/blast/out +@dirrm share/examples/bioperl/blast +@dirrm share/examples/bioperl +@dirrm lib/perl5/site_perl/${MACHINE_ARCH}-netbsd/auto/bp_sw +@dirrm lib/perl5/site_perl/${MACHINE_ARCH}-netbsd/auto/Bio +@dirrm lib/perl5/site_perl/auto/bp_sw +@dirrm lib/perl5/site_perl/Bio/Tools/Blast/Run +@dirrm lib/perl5/site_perl/Bio/Tools/Blast +@dirrm lib/perl5/site_perl/Bio/Tools +@dirrm lib/perl5/site_perl/Bio/Root +@dirrm lib/perl5/site_perl/Bio -- cgit v1.2.3