From b627116d1be4adf4643bfd6954f61b460de6daaf Mon Sep 17 00:00:00 2001 From: jschauma Date: Sat, 27 Sep 2003 22:24:56 +0000 Subject: Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. --- biology/mummer/DESCR | 7 ++++++ biology/mummer/Makefile | 47 +++++++++++++++++++++++++++++++++++++++++ biology/mummer/PLIST | 44 ++++++++++++++++++++++++++++++++++++++ biology/mummer/distinfo | 5 +++++ biology/mummer/patches/patch-aa | 34 +++++++++++++++++++++++++++++ 5 files changed, 137 insertions(+) create mode 100644 biology/mummer/DESCR create mode 100644 biology/mummer/Makefile create mode 100644 biology/mummer/PLIST create mode 100644 biology/mummer/distinfo create mode 100644 biology/mummer/patches/patch-aa (limited to 'biology') diff --git a/biology/mummer/DESCR b/biology/mummer/DESCR new file mode 100644 index 00000000000..d265928f73e --- /dev/null +++ b/biology/mummer/DESCR @@ -0,0 +1,7 @@ +Mummer is a system for aligning whole genome sequences. Using an efficient +data structure called a suffix tree, the system is able rapidly to align +sequences containing millions of nucleotides whether in complete or draft +form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s +of contigs from a shotgun sequencing project with ease, and will align them to +another set of contigs or a genome using the NUCmer program included with the +system. diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile new file mode 100644 index 00000000000..af83ff789c7 --- /dev/null +++ b/biology/mummer/Makefile @@ -0,0 +1,47 @@ +# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 22:24:56 jschauma Exp $ +# + +DISTNAME= MUMmer3.04 +PKGNAME= mummer-3.04 +WRKSRC= ${WRKDIR}/${DISTNAME} +CATEGORIES= biology +MASTER_SITES= ftp://ftp.tigr.org/pub/software/MUMmer/ + +MAINTAINER= hdp@cs.nmsu.edu +HOMEPAGE= http://www.tigr.org/software/mummer/ +COMMENT= System for aligning whole genome sequences + +USE_BUILDLINK2= YES +USE_GNU_TOOLS+= make + +MAKE_ENV+= SH="${SH}" + +do-install: +.for PROGRAM in annotate combineMUMs gaps mgaps mummer repeat-match \ + show-aligns show-coords show-tiling + ${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin +.endfor +.for PROGRAM in postnuc postpro prenuc prepro + ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${PROGRAM} ${PREFIX}/bin +.endfor + ${INSTALL_DATA_DIR} ${PREFIX}/share/mummer +.for SCRIPT in run-mummer1 run-mummer3 nucmer promer exact-tandems \ + 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} \ + ${PREFIX}/share/doc/html/mummer +.endfor + ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/mummer +.for DOC in maxmat3man.pdf 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 +.endfor + +.include "../../lang/perl5/buildlink2.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/mummer/PLIST b/biology/mummer/PLIST new file mode 100644 index 00000000000..ae9522e6679 --- /dev/null +++ b/biology/mummer/PLIST @@ -0,0 +1,44 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $ +bin/annotate +bin/combineMUMs +bin/gaps +bin/mgaps +bin/mummer +bin/postnuc +bin/postpro +bin/prenuc +bin/prepro +bin/repeat-match +bin/show-aligns +bin/show-coords +bin/show-tiling +share/doc/html/mummer/covplot.gif +share/doc/html/mummer/dotplot.gif +share/doc/html/mummer/email.jpg +share/doc/html/mummer/gaps.gif +share/doc/html/mummer/index.html +share/doc/html/mummer/manual_logo.gif +share/doc/html/mummer/mgaps.gif +share/doc/html/mummer/nuc_proex.gif +share/doc/html/mummer/nucex.gif +share/doc/html/mummer/osi.gif +share/doc/html/mummer/pro_proex.gif +share/doc/mummer/maxmat3man.pdf +share/doc/mummer/maxmat3man.tex +share/doc/mummer/maxmat3src.pdf +share/doc/mummer/nucmer.README +share/doc/mummer/optionman.sty +share/doc/mummer/promer.README +share/doc/mummer/run-mummer1.README +share/doc/mummer/run-mummer3.README +share/doc/mummer/skaff.sty +share/mummer/exact-tandems +share/mummer/mummerplot +share/mummer/nucmer +share/mummer/nucmer2xfig +share/mummer/promer +share/mummer/run-mummer1 +share/mummer/run-mummer3 +@dirrm share/mummer +@dirrm share/doc/mummer +@dirrm share/doc/html/mummer diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo new file mode 100644 index 00000000000..5d4bcb3d4d9 --- /dev/null +++ b/biology/mummer/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $ + +SHA1 (MUMmer3.04.tar.gz) = e0f17d535a857bd9b3059d5d0a951621f89041b2 +Size (MUMmer3.04.tar.gz) = 835629 bytes +SHA1 (patch-aa) = 39253c79e7239365dfdcee46c410f234a23c6df0 diff --git a/biology/mummer/patches/patch-aa b/biology/mummer/patches/patch-aa new file mode 100644 index 00000000000..e941dc25546 --- /dev/null +++ b/biology/mummer/patches/patch-aa @@ -0,0 +1,34 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/09/27 22:24:57 jschauma Exp $ + +--- Makefile.orig 2003-07-09 09:49:51.000000000 -0400 ++++ Makefile 2003-09-27 18:15:34.000000000 -0400 +@@ -22,7 +22,7 @@ + # 'make uninstall' alias for 'make clean' (for compatibility) + # + #------------------------------------------------------------------------------- +-SHELL = /bin/sh ++SHELL = ${SH} + VERSION := 3.04 + + +@@ -35,15 +35,12 @@ + TIGR_SRC_DIR := $(TOP_DIR)/src/tigr + KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz + +-CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) +-CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) +-SED := $(filter /%,$(shell /bin/sh -c 'type sed')) ++#CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) ++#CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) ++#SED := $(filter /%,$(shell /bin/sh -c 'type sed')) + CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) +-PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +-AR := $(filter /%,$(shell /bin/sh -c 'type ar')) +- +-CPPFLAGS = -Wall -O3 +-LDFLAGS = ++#PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) ++#AR := $(filter /%,$(shell /bin/sh -c 'type ar')) + + FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README + -- cgit v1.2.3