diff options
Diffstat (limited to 'biology/mummer/Makefile')
| -rw-r--r-- | biology/mummer/Makefile | 56 |
1 files changed, 42 insertions, 14 deletions
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index 4f81b15684b..577fa5a32e1 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -1,26 +1,26 @@ -# $NetBSD: Makefile,v 1.10 2005/12/05 20:49:51 rillig Exp $ +# $NetBSD: Makefile,v 1.11 2006/01/29 19:31:43 schwarz Exp $ # -DISTNAME= MUMmer3.15 -PKGNAME= mummer-3.15 -PKGREVISION= 1 +DISTNAME= MUMmer3.18 +PKGNAME= mummer-3.18 CATEGORIES= biology -MASTER_SITES= ftp://ftp.tigr.org/pub/software/MUMmer/ +MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=mummer/} MAINTAINER= hdp@cs.nmsu.edu -HOMEPAGE= http://www.tigr.org/software/mummer/ +HOMEPAGE= http://mummer.sourceforge.net/ COMMENT= System for aligning whole genome sequences WRKSRC= ${WRKDIR}/${DISTNAME} USE_TOOLS+= gmake perl:run +USE_LANGUAGES= c c++ MAKE_ENV+= SH=${SH:Q} MAKE_ENV+= PERL=${PERL5:Q} INSTALLATION_DIRS= bin do-install: -.for PROGRAM in annotate combineMUMs gaps mgaps mummer repeat-match \ - show-aligns show-coords show-tiling +.for PROGRAM in annotate combineMUMs delta-filter gaps mgaps mummer \ + repeat-match show-aligns show-coords show-snps show-tiling ${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin .endfor .for PROGRAM in postnuc postpro prenuc prepro @@ -28,18 +28,46 @@ do-install: .endfor ${INSTALL_DATA_DIR} ${PREFIX}/share/mummer .for SCRIPT in run-mummer1 run-mummer3 nucmer promer exact-tandems \ - mummerplot nucmer2xfig + mapview mummerplot nucmer2xfig ${INSTALL_SCRIPT} ${WRKSRC}/${SCRIPT} ${PREFIX}/share/mummer .endfor ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/mummer -.for HTML in covplot.gif dotplot.gif email.jpg gaps.gif index.html \ - manual_logo.gif mgaps.gif nuc_proex.gif nucex.gif osi.gif \ - pro_proex.gif - ${INSTALL_DATA} ${WRKSRC}/docs/htmlmanual/${HTML} \ +.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 maxmat3man.tex maxmat3src.pdf nucmer.README \ +.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 |