From ad06e02f5ba547c74dbe5617b236a3d8c37c7cdf Mon Sep 17 00:00:00 2001 From: rillig Date: Thu, 18 Jan 2007 19:13:10 +0000 Subject: Updated mummer to 3.19. Changes since 3.18: - More documentation. --- biology/mummer/Makefile | 64 ++++-------------- biology/mummer/PLIST | 141 +++++++++++++++++++++------------------- biology/mummer/distinfo | 10 +-- biology/mummer/patches/patch-aa | 4 +- 4 files changed, 91 insertions(+), 128 deletions(-) (limited to 'biology') diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index fb7a8d110a2..97281c2c9c3 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -1,9 +1,8 @@ -# $NetBSD: Makefile,v 1.14 2006/12/06 16:52:20 joerg Exp $ +# $NetBSD: Makefile,v 1.15 2007/01/18 19:13:10 rillig Exp $ # -DISTNAME= MUMmer3.18 -PKGNAME= mummer-3.18 -PKGREVISION= 3 +DISTNAME= MUMmer3.19 +PKGNAME= mummer-3.19 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=mummer/} @@ -18,61 +17,20 @@ USE_LANGUAGES= c c++ MAKE_ENV+= SH=${SH:Q} MAKE_ENV+= PERL=${PERL5:Q} MAKE_ENV+= CSH=${TOOLS_PATH.csh:Q} -INSTALLATION_DIRS= bin +INSTALLATION_DIRS= bin share/doc/mummer share/mummer do-install: -.for PROGRAM in annotate combineMUMs delta-filter gaps mgaps mummer \ +.for p in annotate combineMUMs delta-filter gaps mgaps mummer \ repeat-match show-aligns show-coords show-snps show-tiling - ${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/${p} ${PREFIX}/bin .endfor -.for PROGRAM in postnuc postpro prenuc prepro - ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${PROGRAM} ${PREFIX}/bin +.for p in postnuc postpro prenuc prepro + ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${PREFIX}/bin .endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/mummer -.for SCRIPT in run-mummer1 run-mummer3 nucmer promer exact-tandems \ +.for f in run-mummer1 run-mummer3 nucmer promer exact-tandems \ mapview mummerplot nucmer2xfig - ${INSTALL_SCRIPT} ${WRKSRC}/${SCRIPT} ${PREFIX}/share/mummer -.endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer -.for HTML in MUMmer.pdf MUMmer2.pdf MUMmer3.pdf XFiles.pdf \ - applications.html compare.html index.html logo.gif \ - mummer-help.gif mummer-users.gif - ${INSTALL_DATA} ${WRKSRC}/docs/web/${HTML} \ - ${PREFIX}/share/doc/html/mummer -.endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer/examples -.for HTML in dotplot.gif examples_logo.gif index.html mapplot.gif \ - mapview_fig.jpg mummer_ps.jpg - ${INSTALL_DATA} ${WRKSRC}/docs/web/examples/${HTML} \ - ${PREFIX}/share/doc/html/mummer/examples -.endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer/examples/data -.for DATA in B_anthracis_Mslice.fasta B_anthracis_contigs.fasta \ - D_melanogaster_2Rslice.cds D_melanogaster_2Rslice.fasta \ - D_melanogaster_2Rslice.utr D_pseudoobscura_contigs.fasta \ - H_pylori26695_Bslice.fasta H_pylori26695_Eslice.fasta \ - H_pyloriJ99_Bslice.fasta H_pyloriJ99_Eslice.fasta README \ - mapview_0.fig mapview_0.pdf mummer.fplot mummer.gp mummer.mums \ - mummer.ps mummer.rplot mummer1.align mummer1.errorsgaps \ - mummer1.gaps mummer1.out mummer3.align mummer3.errorsgaps \ - mummer3.gaps mummer3.out nucmer.cluster nucmer.coords \ - nucmer.delta nucmer.snps nucmer.tiling promer.aligns \ - promer.cluster promer.coords promer.delta - ${INSTALL_DATA} ${WRKSRC}/docs/web/examples/data/${DATA} \ - ${PREFIX}/share/doc/html/mummer/examples/data -.endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer/manual -.for HTML in covplot.gif dotplot.gif gaps.gif index.html \ - manual_logo.gif mgaps.gif multiplota.gif multiplotb.gif \ - nuc_proex.gif nucex.gif osi.gif pro_proex.gif - ${INSTALL_DATA} ${WRKSRC}/docs/web/manual/${HTML} \ - ${PREFIX}/share/doc/html/mummer/manual -.endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/mummer -.for DOC in mapview.README maxmat3man.tex maxmat3src.pdf nucmer.README \ - optionman.sty promer.README run-mummer1.README run-mummer3.README \ - skaff.sty - ${INSTALL_DATA} ${WRKSRC}/docs/${DOC} ${PREFIX}/share/doc/mummer + ${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/share/mummer .endfor + cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * ${PREFIX}/share/doc/mummer .include "../../mk/bsd.pkg.mk" diff --git a/biology/mummer/PLIST b/biology/mummer/PLIST index aa8ba4fdc12..32948e95ba5 100644 --- a/biology/mummer/PLIST +++ b/biology/mummer/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.4 2006/06/21 19:01:12 minskim Exp $ +@comment $NetBSD: PLIST,v 1.5 2007/01/18 19:13:10 rillig Exp $ bin/annotate bin/combineMUMs bin/delta-filter @@ -14,69 +14,8 @@ bin/show-aligns bin/show-coords bin/show-snps bin/show-tiling -share/doc/html/mummer/MUMmer.pdf -share/doc/html/mummer/MUMmer2.pdf -share/doc/html/mummer/MUMmer3.pdf -share/doc/html/mummer/XFiles.pdf -share/doc/html/mummer/applications.html -share/doc/html/mummer/compare.html -share/doc/html/mummer/index.html -share/doc/html/mummer/logo.gif -share/doc/html/mummer/mummer-help.gif -share/doc/html/mummer/mummer-users.gif -share/doc/html/mummer/examples/dotplot.gif -share/doc/html/mummer/examples/examples_logo.gif -share/doc/html/mummer/examples/index.html -share/doc/html/mummer/examples/mapplot.gif -share/doc/html/mummer/examples/mapview_fig.jpg -share/doc/html/mummer/examples/mummer_ps.jpg -share/doc/html/mummer/examples/data/B_anthracis_Mslice.fasta -share/doc/html/mummer/examples/data/B_anthracis_contigs.fasta -share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.cds -share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.fasta -share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.utr -share/doc/html/mummer/examples/data/D_pseudoobscura_contigs.fasta -share/doc/html/mummer/examples/data/H_pylori26695_Bslice.fasta -share/doc/html/mummer/examples/data/H_pylori26695_Eslice.fasta -share/doc/html/mummer/examples/data/H_pyloriJ99_Bslice.fasta -share/doc/html/mummer/examples/data/H_pyloriJ99_Eslice.fasta -share/doc/html/mummer/examples/data/README -share/doc/html/mummer/examples/data/mapview_0.fig -share/doc/html/mummer/examples/data/mapview_0.pdf -share/doc/html/mummer/examples/data/mummer.fplot -share/doc/html/mummer/examples/data/mummer.gp -share/doc/html/mummer/examples/data/mummer.mums -share/doc/html/mummer/examples/data/mummer.ps -share/doc/html/mummer/examples/data/mummer.rplot -share/doc/html/mummer/examples/data/mummer1.align -share/doc/html/mummer/examples/data/mummer1.errorsgaps -share/doc/html/mummer/examples/data/mummer1.gaps -share/doc/html/mummer/examples/data/mummer1.out -share/doc/html/mummer/examples/data/mummer3.align -share/doc/html/mummer/examples/data/mummer3.errorsgaps -share/doc/html/mummer/examples/data/mummer3.gaps -share/doc/html/mummer/examples/data/mummer3.out -share/doc/html/mummer/examples/data/nucmer.cluster -share/doc/html/mummer/examples/data/nucmer.coords -share/doc/html/mummer/examples/data/nucmer.delta -share/doc/html/mummer/examples/data/nucmer.snps -share/doc/html/mummer/examples/data/nucmer.tiling -share/doc/html/mummer/examples/data/promer.aligns -share/doc/html/mummer/examples/data/promer.cluster -share/doc/html/mummer/examples/data/promer.coords -share/doc/html/mummer/examples/data/promer.delta -share/doc/html/mummer/manual/covplot.gif -share/doc/html/mummer/manual/dotplot.gif -share/doc/html/mummer/manual/gaps.gif -share/doc/html/mummer/manual/index.html -share/doc/html/mummer/manual/manual_logo.gif -share/doc/html/mummer/manual/mgaps.gif -share/doc/html/mummer/manual/multiplota.gif -share/doc/html/mummer/manual/multiplotb.gif -share/doc/html/mummer/manual/nuc_proex.gif -share/doc/html/mummer/manual/nucex.gif -share/doc/html/mummer/manual/osi.gif -share/doc/html/mummer/manual/pro_proex.gif +share/doc/mummer/README +share/doc/mummer/differences.README share/doc/mummer/mapview.README share/doc/mummer/maxmat3man.tex share/doc/mummer/maxmat3src.pdf @@ -86,6 +25,72 @@ share/doc/mummer/promer.README share/doc/mummer/run-mummer1.README share/doc/mummer/run-mummer3.README share/doc/mummer/skaff.sty +share/doc/mummer/web/MUMmer.pdf +share/doc/mummer/web/MUMmer2.pdf +share/doc/mummer/web/MUMmer3.pdf +share/doc/mummer/web/XFiles.pdf +share/doc/mummer/web/applications.html +share/doc/mummer/web/compare.html +share/doc/mummer/web/examples/data/B_anthracis_Mslice.fasta +share/doc/mummer/web/examples/data/B_anthracis_contigs.fasta +share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.cds +share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.fasta +share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.utr +share/doc/mummer/web/examples/data/D_pseudoobscura_contigs.fasta +share/doc/mummer/web/examples/data/H_pylori26695_Bslice.fasta +share/doc/mummer/web/examples/data/H_pylori26695_Eslice.fasta +share/doc/mummer/web/examples/data/H_pyloriJ99_Bslice.fasta +share/doc/mummer/web/examples/data/H_pyloriJ99_Eslice.fasta +share/doc/mummer/web/examples/data/README +share/doc/mummer/web/examples/data/mapview_0.fig +share/doc/mummer/web/examples/data/mapview_0.pdf +share/doc/mummer/web/examples/data/mummer.fplot +share/doc/mummer/web/examples/data/mummer.gp +share/doc/mummer/web/examples/data/mummer.mums +share/doc/mummer/web/examples/data/mummer.ps +share/doc/mummer/web/examples/data/mummer.rplot +share/doc/mummer/web/examples/data/mummer1.align +share/doc/mummer/web/examples/data/mummer1.errorsgaps +share/doc/mummer/web/examples/data/mummer1.gaps +share/doc/mummer/web/examples/data/mummer1.out +share/doc/mummer/web/examples/data/mummer3.align +share/doc/mummer/web/examples/data/mummer3.errorsgaps +share/doc/mummer/web/examples/data/mummer3.gaps +share/doc/mummer/web/examples/data/mummer3.out +share/doc/mummer/web/examples/data/nucmer.cluster +share/doc/mummer/web/examples/data/nucmer.coords +share/doc/mummer/web/examples/data/nucmer.delta +share/doc/mummer/web/examples/data/nucmer.snps +share/doc/mummer/web/examples/data/nucmer.tiling +share/doc/mummer/web/examples/data/promer.aligns +share/doc/mummer/web/examples/data/promer.cluster +share/doc/mummer/web/examples/data/promer.coords +share/doc/mummer/web/examples/data/promer.delta +share/doc/mummer/web/examples/dotplot.gif +share/doc/mummer/web/examples/examples_logo.gif +share/doc/mummer/web/examples/index.html +share/doc/mummer/web/examples/mapplot.gif +share/doc/mummer/web/examples/mapview_fig.jpg +share/doc/mummer/web/examples/mummer_ps.jpg +share/doc/mummer/web/index.html +share/doc/mummer/web/logo.gif +share/doc/mummer/web/manual/AlignmentTypes.odg +share/doc/mummer/web/manual/AlignmentTypes.pdf +share/doc/mummer/web/manual/covplot.gif +share/doc/mummer/web/manual/dotplot.gif +share/doc/mummer/web/manual/gaps.gif +share/doc/mummer/web/manual/index.html +share/doc/mummer/web/manual/manual_logo.gif +share/doc/mummer/web/manual/mapplot.gif +share/doc/mummer/web/manual/mgaps.gif +share/doc/mummer/web/manual/multiplota.gif +share/doc/mummer/web/manual/multiplotb.gif +share/doc/mummer/web/manual/nuc_proex.gif +share/doc/mummer/web/manual/nucex.gif +share/doc/mummer/web/manual/osi.gif +share/doc/mummer/web/manual/pro_proex.gif +share/doc/mummer/web/mummer-help.gif +share/doc/mummer/web/mummer-users.gif share/mummer/exact-tandems share/mummer/mapview share/mummer/mummerplot @@ -95,8 +100,8 @@ share/mummer/promer share/mummer/run-mummer1 share/mummer/run-mummer3 @dirrm share/mummer +@dirrm share/doc/mummer/web/manual +@dirrm share/doc/mummer/web/examples/data +@dirrm share/doc/mummer/web/examples +@dirrm share/doc/mummer/web @dirrm share/doc/mummer -@dirrm share/doc/html/mummer/examples/data -@dirrm share/doc/html/mummer/examples -@dirrm share/doc/html/mummer/manual -@dirrm share/doc/html/mummer diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo index b7e98faead1..45af2ccb057 100644 --- a/biology/mummer/distinfo +++ b/biology/mummer/distinfo @@ -1,9 +1,9 @@ -$NetBSD: distinfo,v 1.7 2006/12/06 16:52:20 joerg Exp $ +$NetBSD: distinfo,v 1.8 2007/01/18 19:13:10 rillig Exp $ -SHA1 (MUMmer3.18.tar.gz) = 484846f7ff68e19bc0e0deca92254fd423947a9f -RMD160 (MUMmer3.18.tar.gz) = 7361a90d28e2432a9163e0745ab854dfd31cf306 -Size (MUMmer3.18.tar.gz) = 3069437 bytes -SHA1 (patch-aa) = 707f0466ac20b58feb22a5fd525f5f8d9df31dac +SHA1 (MUMmer3.19.tar.gz) = 8906bab6bd43b307461de8b5f44122a115799533 +RMD160 (MUMmer3.19.tar.gz) = 54f3c692efb8bde7762c48186919754f2a8c178c +Size (MUMmer3.19.tar.gz) = 3141991 bytes +SHA1 (patch-aa) = e40b6538b259475def39cd8008af37d0a08e1555 SHA1 (patch-ab) = af42da79fd287786cb83efa9c9b4fc8025abd728 SHA1 (patch-ac) = 7f0f16bdd83bc80833f1ffdcfe1bad7c2ee76eec SHA1 (patch-ad) = 0804b2c966d7035c23444c4f72e1d93e45805bcf diff --git a/biology/mummer/patches/patch-aa b/biology/mummer/patches/patch-aa index 20723ca7f72..4f3836d2822 100644 --- a/biology/mummer/patches/patch-aa +++ b/biology/mummer/patches/patch-aa @@ -1,4 +1,4 @@ -$NetBSD: patch-aa,v 1.4 2006/12/06 16:52:20 joerg Exp $ +$NetBSD: patch-aa,v 1.5 2007/01/18 19:13:10 rillig Exp $ --- Makefile.orig 2003-07-09 09:49:51.000000000 -0400 +++ Makefile 2003-09-27 18:15:34.000000000 -0400 @@ -8,7 +8,7 @@ $NetBSD: patch-aa,v 1.4 2006/12/06 16:52:20 joerg Exp $ #------------------------------------------------------------------------------- -SHELL = /bin/sh +SHELL = ${SH} - VERSION := 3.18 + VERSION := 3.19 @@ -35,15 +35,12 @@ -- cgit v1.2.3