Attachment #48577 for bug #74333

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# Date created:		31 July 2000
# Whom:	      		Johann Visagie <johann@egenetics.com>
#
# $FreeBSD: ports/biology/emboss/Makefile,v 1.39 2004/06/23 08:20:21 vs Exp $
#

PORTNAME=	emboss
PORTVERSION=	2.9.0
PORTREVISION=	3
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTNAME=	${PORTNAME:U}-${PORTVERSION}
DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
DIST_SUBDIR=	${PORTNAME}
EXTRACT_ONLY=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}

MAINTAINER=	fernan@iib.unsam.edu.ar
COMMENT=	A collection of open source tools for genetic sequence analysis

BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
		primer3:${PORTSDIR}/biology/primer3
LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
		png.5:${PORTSDIR}/graphics/png

USE_SUBMAKE=	yes
USE_GMAKE=	yes
GNU_CONFIGURE=	yes
USE_LIBTOOL_VER=15
INSTALLS_SHLIB=	yes
USE_XLIB=	yes
USE_MOTIF=	yes
USE_REINPLACE=	yes
PKGMESSAGE=	${WRKDIR}/pkg-message

.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
.endif

CONFIGURE_ENV+=	CPPFLAGS="-I${LOCALBASE}/include" \
		LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
SCRIPTS_ENV+=	WRKDIRPREFIX="${WRKDIRPREFIX}" \
		MKDIR="${MKDIR}" RM="${RM}"

WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
EMNU_VERSION=	1.0.5
HMMER_VERSION=	2.1.1
MEME_VERSION=	2.3.1
MSE_VERSION=	0.0.4
TOPO_VERSION=	0.1
PHYLIP_VERSION=	3.573c
DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template

.for app in EMNU HMMER MEME MSE PHYLIP TOPO
SCRIPTS_ENV+=	${app}_VERSION="${${app}_VERSION}"
.if defined(WITH_${app})
APPLIST+=	${app}
${app}_WRKSRC=	${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
DISTFILES+=	${${app}_DISTFILE}
PLIST_${app}=	""
.else
PLIST_${app}=	"@comment "
.endif
PLIST_SUB+=	PLIST_${app}=${PLIST_${app}}
.endfor

# Jemboss support is a work in progress.
#
#.if defined(WITH_JEMBOSS)
#USE_JAVA=	1.3+
#CONFIGURE_ARGS+=	--with-java=${JAVA_HOME}/include \
#			--with-javaos=${JAVA_HOME}/include/${JAVA_OS:L}
#CONFIGURE_ENV+=	PATH=${PATH}:${JAVA_HOME}/bin
#MAKE_ENV+=	PATH=${PATH}:${JAVA_HOME}/bin
#JEMBOSS_WRKSRC=	${WRKSRC}/jemboss
#.endif

pre-fetch:
	@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}

post-extract:
.for app in ${APPLIST}
	@ ${MKDIR} ${EMBASSY_WRKDIR}
	@ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \
	  ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS}
	@ if [ `id -u` = 0 ]; then \
	    ${CHMOD} -R ug-s ${${app}_WRKSRC}; \
	    ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \
	  fi
.endfor

post-patch:
.if !defined(NOPORTDOCS)
.for DIR in ${DOC_DIRS}
	${REINPLACE_CMD} -e \
	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
	  ${WRKSRC}/${DIR}/Makefile.in
.endfor
.endif
post-configure:
.for app in ${APPLIST}
	@ cd ${${app}_WRKSRC} && \
	  ${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \
	  CXXFLAGS="${CXXFLAGS}" \
	  INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \
	  INSTALL_DATA="${INSTALL_DATA}" \
	  INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
	  INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
	  ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
.endfor

post-build:
.for app in ${APPLIST}
	@ cd ${${app}_WRKSRC} && \
	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
	  ${MAKE_ARGS}
.endfor
#.if defined(WITH_JEMBOSS)
#	@ cd ${JEMBOSS_WRKSRC} && \
#	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
#	  ${MAKE_ARGS}
#.endif

post-install:
	@ cd ${WRKSRC} && \
	${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
	  ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
	  ${CHOWN} ${SHAREOWN}:${SHAREGRP} \
	  ${PREFIX}/etc/emboss.default.sample
	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
	  pkg-message > ${PKGMESSAGE}
.if !defined(BATCH)
	@ ${CAT} ${PKGMESSAGE}
.endif

post-clean:
	@ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc

.include <bsd.port.mk>

Lines 1-7 Link Here

(-)emboss/distinfo (-7 / +2 lines)
1	MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad	1	MD5 (EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472
2	MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66	2	SIZE (EMBOSS-2.9.0.tar.gz) = 14479274
3	MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21
4	MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c
5	MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9
6	MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084
7	MD5 (emboss/TOPO-0.1.tar.gz) = a5131f2e0d58e06ce071250b62cbe65a

Lines 1-26 Link Here

(-)emboss/files/patch-aa (-5 lines)
1	Add ${PREFIX}/etc as an acceptable location for emboss.default. (I'm still
2	waiting for this to be incorporated into an official release of EMBOSS.)
3
4	The port installs ${PREFIX}/etc/emboss.default.sample
5

Lines 1-11 Link Here

(-)emboss/files/patch-ajax::ajjava.c (-11 lines)
1	--- ajax/ajjava.c.orig Thu May 2 22:06:08 2002
2	+++ ajax/ajjava.c Sun May 26 09:14:20 2002
3	@@ -75,7 +75,7 @@
4	#endif
5
6	#ifndef __ppc__
7	-#include <crypt.h>
8	+#include <unistd.h>
9	#endif
10
11

Lines 1-11 Link Here

(-)emboss/files/patch-configure (-11 lines)
1	--- configure.orig Mon Jan 22 23:28:17 2001
2	+++ configure Thu Jan 25 19:07:33 2001
3	@@ -1473,7 +1473,7 @@
4
5
6
7	-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
8	+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
9
10	#AC_PROG_CXX
11	for ac_prog in mawk gawk nawk awk




--- emboss/emboss.default.template.orig	Thu May 24 19:36:39 2001
+++ emboss/emboss.default.template	Wed May 30 10:23:48 2001
@@ -1,9 +1,31 @@
-#SET emboss_tempdata name_of_emboss_test_database_directory
+#####################################################
+### Configuration options for FreeBSD EMBOSS port ###
+#####################################################
 
-# Logfile - set this to a file that any user can append to
-# and EMBOSS applications will automatically write log information
+# The directory where EMBOSS expects to find run-time
+# databases.  This is the compiled-in default - change
+# only if you know what you're doing!
+#
+#SET emboss_data %%PREFIX%%/share/EMBOSS/data
 
-#SET emboss_logfile /packages/emboss/emboss/log
+# This is an alias which is internal to this
+# configuration file and is set here merely as a
+# convenience.  It points to the location where you
+# have placed your local databases (this will differ
+# from site to site).
+#
+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
+
+# Logfile.  If this is uncommented and set to a file
+# that any user can append to, EMBOSS applications
+# will automatically log usage information.
+#
+#SET emboss_logfile /var/log/emboss.log
+
+
+###########################################
+### Configuration options for databases ###
+###########################################
 
 # swissprot (Puffer fish entries)
 # =========

Lines 15-21 Link Here

(-)emboss/pkg-message (-1 / +2 lines)
15	system-wide emboss.default.	15	system-wide emboss.default.
16		16
17	Online EMBOSS documentation is available at:	17	Online EMBOSS documentation is available at:
18	http://www.uk.embnet.org/Software/EMBOSS/general.html	18	http://www.uk.embnet.org/Software/EMBOSS/userdoc.html
19	http://www.uk.embnet.org/Software/EMBOSS/Doc/	19	http://www.uk.embnet.org/Software/EMBOSS/Doc/
		20	http://emboss.sourceforge.net/docs/
20		21
21	--------------------------------------------------------------------------	22	--------------------------------------------------------------------------




bin/aaindexextract
%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
%%PLIST_HMMER%%bin/ealistat
%%PLIST_HMMER%%bin/ehmmalign
%%PLIST_HMMER%%bin/ehmmbuild
%%PLIST_HMMER%%bin/ehmmcalibrate
%%PLIST_HMMER%%bin/ehmmconvert
%%PLIST_HMMER%%bin/ehmmemit
%%PLIST_HMMER%%bin/ehmmfetch
%%PLIST_HMMER%%bin/ehmmindex
%%PLIST_HMMER%%bin/ehmmpfam
%%PLIST_HMMER%%bin/ehmmsearch
%%PLIST_HMMER%%lib/libhmmer.a
%%PLIST_HMMER%%lib/libhmmer.la
%%PLIST_HMMER%%lib/libhmmer.so
%%PLIST_HMMER%%lib/libhmmer.so.2
%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
%%PLIST_MEME%%bin/meme
%%PLIST_MEME%%lib/libmeme.a
%%PLIST_MEME%%lib/libmeme.la
%%PLIST_MEME%%lib/libmeme.so
%%PLIST_MEME%%lib/libmeme.so.2
%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
%%PLIST_MSE%%bin/mse
%%PLIST_MSE%%lib/libckit.a
%%PLIST_MSE%%lib/libckit.la
%%PLIST_MSE%%lib/libckit.so
%%PLIST_MSE%%lib/libckit.so.1
%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
%%PLIST_PHYLIP%%bin/eclique
%%PLIST_PHYLIP%%bin/econsense
%%PLIST_PHYLIP%%bin/econtml
%%PLIST_PHYLIP%%bin/econtrast
%%PLIST_PHYLIP%%bin/ednacomp
%%PLIST_PHYLIP%%bin/ednadist
%%PLIST_PHYLIP%%bin/ednainvar
%%PLIST_PHYLIP%%bin/ednaml
%%PLIST_PHYLIP%%bin/ednamlk
%%PLIST_PHYLIP%%bin/ednapars
%%PLIST_PHYLIP%%bin/ednapenny
%%PLIST_PHYLIP%%bin/edollop
%%PLIST_PHYLIP%%bin/edolpenny
%%PLIST_PHYLIP%%bin/efactor
%%PLIST_PHYLIP%%bin/efitch
%%PLIST_PHYLIP%%bin/egendist
%%PLIST_PHYLIP%%bin/ekitsch
%%PLIST_PHYLIP%%bin/emix
%%PLIST_PHYLIP%%bin/eneighbor
%%PLIST_PHYLIP%%bin/epenny
%%PLIST_PHYLIP%%bin/eprotdist
%%PLIST_PHYLIP%%bin/eprotpars
%%PLIST_PHYLIP%%bin/erestml
%%PLIST_PHYLIP%%bin/eseqboot
%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
%%PLIST_TOPO%%bin/topo
%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
bin/abiview
bin/acdc
bin/acdpretty
bin/acdtable
bin/acdtrace
bin/acdvalid
bin/antigenic
bin/backtranseq
bin/banana

bin/coderet
bin/compseq
bin/cons
bin/contacts
bin/cpgplot
bin/cpgreport
bin/cusp

bin/dbigcg
bin/degapseq
bin/descseq
bin/dichet
bin/diffseq
bin/digest
bin/distmat
bin/domainer
bin/dotmatcher
bin/dotpath
bin/dottup

bin/emma
bin/emowse
bin/entret
bin/epestfind
bin/eprimer3
bin/equicktandem
bin/est2genome
bin/etandem

bin/infoalign
bin/infoseq
bin/isochore
bin/jembossctl
bin/lindna
bin/listor
bin/marscan

bin/megamerger
bin/merger
bin/msbar
bin/mwcontam
bin/mwfilter
bin/needle
bin/newcpgreport
bin/newcpgseek
bin/newseq
bin/noreturn
bin/notseq
bin/noreturn
bin/nthseq
bin/octanol
bin/oddcomp

bin/prophet
bin/prosextract
bin/pscan
bin/psiphi
bin/rebaseextract
bin/recoder
bin/redata

bin/restover
bin/restrict
bin/revseq
bin/runJemboss.csh
bin/scopalign
bin/scope
bin/seealso
bin/seqmatchall
bin/seqret

bin/showseq
bin/shuffleseq
bin/sigcleave
bin/siggen
bin/sigscan
bin/silent
bin/sirna
bin/sixpack
bin/skipseq
bin/splitter
bin/stretcher
bin/stssearch
bin/supermatcher
bin/swissparse
bin/syco
bin/tcode
bin/textsearch
bin/tfextract
bin/tfm
bin/tfscan
bin/tmap
bin/tranalign
bin/transeq
bin/trimest
bin/trimseq
bin/twofeat
bin/union
bin/vectorstrip
bin/water
bin/whichdb
bin/wobble
bin/wordcount
bin/wordmatch
bin/wossname
bin/yank
bin/runJemboss.csh
etc/emboss.default.sample
include/drivers.h
include/pdf.h
include/plcore.h
include/plevent.h
include/plplotP.h
include/plxwd.h
include/metadefs.h
include/plConfig.h
include/pldebug.h
include/plplot.h
include/plstrm.h
include/plDevs.h
include/ajax.h
include/ajarch.h
include/ajdefine.h
include/ajacd.h
include/ajalign.h
include/ajarr.h
include/ajassert.h
include/ajbase.h
include/ajcall.h
include/ajcod.h
include/ajdan.h
include/ajdmx.h
include/ajdomain.h
include/ajexcept.h
include/ajfeat.h
include/ajfeatdata.h
include/ajfile.h
include/ajfmt.h
include/ajgraph.h
include/ajgraphxml.h
include/ajgraphstruct.h
include/ajhist.h
include/ajjava.h
include/ajlist.h
include/ajmath.h
include/ajmatrices.h
include/ajmem.h
include/ajmess.h
include/ajnam.h
include/ajnexus.h
include/ajpdb.h
include/ajpdbio.h
include/ajphylo.h
include/ajrange.h
include/ajreg.h
include/ajreport.h
include/ajseq.h
include/ajseqabi.h
include/ajseqdata.h
include/ajseqdb.h
include/ajseqread.h
include/ajseqtype.h
include/ajseqwrite.h
include/ajsort.h
include/ajstr.h
include/ajsys.h
include/ajtable.h
include/ajtime.h
include/ajtranslate.h
include/ajtree.h
include/ajutil.h
include/ajvector.h
include/pcre.h
include/pcre_chartables.c
include/pcre_config.h
include/pcre_get.c
include/pcre_printint.c
include/pcre_internal.h
include/pcreposix.h
include/emboss.h
include/embaln.h
include/embcom.h
include/embcons.h
include/embdata.h
include/embdbi.h
include/embdmx.h
include/embest.h
include/embexit.h
include/embgotoh.h
include/embgroup.h
include/embiep.h
include/embindex.h
include/embinit.h
include/embmat.h
include/embmisc.h
include/embmol.h
include/embnmer.h
include/embpat.h
include/embprop.h
include/embpdb.h
include/embdomain.h
include/embsig.h
include/embread.h
include/embshow.h
include/embword.h
lib/libplplot.so.5
lib/libplplot.so
lib/libplplot.a
lib/libajax.so.1
lib/libajax.so
lib/libajax.a
lib/libajaxg.so
lib/libajaxg.so.1
lib/libajaxg.so
lib/libajaxg.a
lib/libnucleus.so
lib/libnucleus.so.1
lib/libnucleus.so
lib/libnucleus.a
%%PORTDOCS%%DOCSDIR%%/manuals/admin.sty
%%PORTDOCS%%DOCSDIR%%/manuals/admin.tex
%%PORTDOCS%%DOCSDIR%%/manuals/admin.aux
%%PORTDOCS%%DOCSDIR%%/manuals/admin.dvi
%%PORTDOCS%%DOCSDIR%%/manuals/admin.log
%%PORTDOCS%%DOCSDIR%%/manuals/admin.pdf
%%PORTDOCS%%DOCSDIR%%/manuals/admin.ps
%%PORTDOCS%%DOCSDIR%%/manuals/admin.toc
%%PORTDOCS%%DOCSDIR%%/manuals/adminguide.tar.gz
%%PORTDOCS%%DOCSDIR%%/manuals/domainatrix.doc
%%PORTDOCS%%DOCSDIR%%/manuals/program.ps.gz
%%PORTDOCS%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
%%PORTDOCS%%DOCSDIR%%/manuals/emboss_qg.pdf
%%PORTDOCS%%DOCSDIR%%/manuals/emboss_qg.ps
%%PORTDOCS%%DOCSDIR%%/manuals/emboss.sty
%%PORTDOCS%%DOCSDIR%%/manuals/fdl.txt
%%PORTDOCS%%DOCSDIR%%/programs/html/lindna.html
%%PORTDOCS%%DOCSDIR%%/programs/html/listor.html
%%PORTDOCS%%DOCSDIR%%/programs/html/marscan.html
%%PORTDOCS%%DOCSDIR%%/programs/html/maskfeat.html
%%PORTDOCS%%DOCSDIR%%/programs/html/maskseq.html
%%PORTDOCS%%DOCSDIR%%/programs/html/matcher.html
%%PORTDOCS%%DOCSDIR%%/programs/html/megamerger.html
%%PORTDOCS%%DOCSDIR%%/programs/html/merger.html
%%PORTDOCS%%DOCSDIR%%/programs/html/mix.html
%%PORTDOCS%%DOCSDIR%%/programs/html/msbar.html
%%PORTDOCS%%DOCSDIR%%/programs/html/mse.html
%%PORTDOCS%%DOCSDIR%%/programs/html/mwcontam.html
%%PORTDOCS%%DOCSDIR%%/programs/html/mwfilter.html
%%PORTDOCS%%DOCSDIR%%/programs/html/needle.html
%%PORTDOCS%%DOCSDIR%%/programs/html/neighbor.html
%%PORTDOCS%%DOCSDIR%%/programs/html/newcpgreport.html
%%PORTDOCS%%DOCSDIR%%/programs/html/newcpgseek.html
%%PORTDOCS%%DOCSDIR%%/programs/html/newseq.html
%%PORTDOCS%%DOCSDIR%%/programs/html/noreturn.html
%%PORTDOCS%%DOCSDIR%%/programs/html/notseq.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nthseq.html
%%PORTDOCS%%DOCSDIR%%/programs/html/penny.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_composition_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_primers_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/octanol.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/nucleic_translation_group.html
%%PORTDOCS%%DOCSDIR%%/programs/html/oddcomp.html
%%PORTDOCS%%DOCSDIR%%/programs/html/palindrome.html
%%PORTDOCS%%DOCSDIR%%/programs/html/pasteseq.html
%%PORTDOCS%%DOCSDIR%%/programs/html/patmatdb.html
%%PORTDOCS%%DOCSDIR%%/programs/html/patmatmotifs.html
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share/doc/EMBOSS/tutorials/emboss_tutorial.ps.gz
share/doc/EMBOSS/tutorials/emboss_tutorial.tex
share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
share/doc/EMBOSS/tutorials/pepinfo2.ps.gz
share/doc/EMBOSS/tutorials/plotorf.ps.gz
share/doc/EMBOSS/tutorials/tmap.ps.gz
@dirrm share/doc/EMBOSS/tutorials
@dirrm share/doc/EMBOSS/programs/text
@dirrm share/doc/EMBOSS/programs/html
@dirrm share/doc/EMBOSS/programs
@dirrm share/doc/EMBOSS/manuals
@dirrm share/doc/EMBOSS
@dirrm share/EMBOSS/test/wormpep
@dirrm share/EMBOSS/test/swnew
@dirrm share/EMBOSS/test/swiss
@dirrm share/EMBOSS/test/pir
@dirrm share/EMBOSS/test/genbank
@dirrm share/EMBOSS/test/gb
@dirrm share/EMBOSS/test/pir
@dirrm share/EMBOSS/test/swiss
@dirrm share/EMBOSS/test/swnew
@dirrm share/EMBOSS/test/wormpep
@dirrm share/EMBOSS/test
@dirrm share/EMBOSS/jemboss/utils
@dirrm share/EMBOSS/jemboss/resources
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/soap
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/server
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/programs
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss
@dirrm share/EMBOSS/jemboss/org/emboss
@dirrm share/EMBOSS/jemboss/org
@dirrm share/EMBOSS/jemboss/lib
@dirrm share/EMBOSS/jemboss/images
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/filetree
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss
@dirrm share/EMBOSS/jemboss/api/org/emboss
@dirrm share/EMBOSS/jemboss/api/org
@dirrm share/EMBOSS/jemboss/api
@dirrm share/EMBOSS/jemboss/images
@dirrm share/EMBOSS/jemboss/lib/axis
@dirrm share/EMBOSS/jemboss/lib
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/editor
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/draw
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/programs
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/server
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/soap
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss
@dirrm share/EMBOSS/jemboss/org/emboss
@dirrm share/EMBOSS/jemboss/org
@dirrm share/EMBOSS/jemboss/resources
@dirrm share/EMBOSS/jemboss/utils
@dirrm share/EMBOSS/jemboss
@dirrm share/EMBOSS/data/REBASE
@dirrm share/EMBOSS/data/PROSITE
@dirrm share/EMBOSS/data/PRINTS
@dirrm share/EMBOSS/data/CODONS
@dirrm share/EMBOSS/data
@dirrm share/EMBOSS/acd
@dirrm share/EMBOSS




#!/bin/sh

if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
  exit
fi

if [ "${BATCH}" ]; then
  set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\"
else
  /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
  --checklist "\n\
These third party applications have been adapted to
function as part of EMBOSS.\n
Please select EMBASSY applications to install:" -1 -1 6 \
EMNU	"v${EMNU_VERSION} - Text-based menu" ON \
HMMER	"v${HMMER_VERSION} - HMM alignment" ON \
MEME	"v${MEME_VERSION} - Motif detection" ON \
MSE	"v${MSE_VERSION} - Phylogeny inference" ON \
PHYLIP	"v${PHYLIP_VERSION} - Sequence editor" ON \
TOPO	"v${TOPO_VERSION} - Transmembrane display" ON \
2> /tmp/checklist.tmp.$$

  retval=$?

  if [ -s /tmp/checklist.tmp.$$ ]; then
    set `cat /tmp/checklist.tmp.$$`
  fi
  ${RM} -f /tmp/checklist.tmp.$$

  case $retval in
    0)
      if [ -z "$*" ]; then
        echo "Nothing selected"
      fi
    ;;
    1)
      echo "Cancel pressed."
      exit 1
    ;;
  esac
fi

${MKDIR} ${WRKDIRPREFIX}${CURDIR}
exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc

while [ "$1" ]; do
  case $1 in
    \"EMNU\")
      echo "WITH_EMNU=	yes"
    ;;
    \"HMMER\")
      echo "WITH_HMMER=	yes"
    ;;
    \"MEME\")
      echo "WITH_MEME=	yes"
    ;;
    \"MSE\")
      echo "WITH_MSE=	yes"
    ;;
    \"PHYLIP\")
      echo "WITH_PHYLIP=	yes"
    ;;
    \"TOPO\")
      echo "WITH_TOPO=	yes"
    ;;
    *)
      echo "Invalid option(s): $*" > /dev/stderr
      ${RM} -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
      exit 1
    ;;
  esac
  shift
done

Return to bug 74333

Lines 2-142 Link Here

(-)emboss/Makefile (-107 / +22 lines)
2	# Date created: 31 July 2000	2	# Date created: 31 July 2000
3	# Whom: Johann Visagie <johann@egenetics.com>	3	# Whom: Johann Visagie <johann@egenetics.com>
4	#	4	#
5	# $FreeBSD: ports/biology/emboss/Makefile,v 1.40 2004/11/20 07:40:43 linimon Exp $	5	# $FreeBSD: ports/biology/emboss/Makefile,v 1.39 2004/06/23 08:20:21 vs Exp $
6	#	6	#
7		7
8	PORTNAME= emboss	8	PORTNAME= emboss
9	PORTVERSION= 2.4.1	9	PORTVERSION= 2.9.0
10	PORTREVISION= 3
11	CATEGORIES= biology	10	CATEGORIES= biology
12	MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/old/ \	11	MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
13	ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old/	12	ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
14	# ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/	13	ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
		14	DISTNAME= ${PORTNAME:U}-${PORTVERSION}
15	DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}	15	DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
16	DIST_SUBDIR= ${PORTNAME}
17	EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
18		16
19	MAINTAINER= ports@FreeBSD.org	17	MAINTAINER= fernan@iib.unsam.edu.ar
20	COMMENT= A collection of open source tools for genetic sequence analysis	18	COMMENT= A collection of open source tools for genetic sequence analysis
21		19
22	LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd	20	BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \
		21	primer3:${PORTSDIR}/biology/primer3
		22	LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \
		23	png.5:${PORTSDIR}/graphics/png
23		24
24	USE_SUBMAKE= yes	25	USE_SUBMAKE= yes
25	USE_GMAKE= yes	26	USE_GMAKE= yes
26	GNU_CONFIGURE= yes	27	GNU_CONFIGURE= yes
		28	USE_LIBTOOL_VER=15
27	INSTALLS_SHLIB= yes	29	INSTALLS_SHLIB= yes
28	USE_XLIB= yes	30	USE_XLIB= yes
29	USE_MOTIF= yes	31	USE_MOTIF= yes
30	USE_PERL5_BUILD=yes	32	USE_REINPLACE= yes
31	PKGMESSAGE= ${WRKDIR}/pkg-message	33	PKGMESSAGE= ${WRKDIR}/pkg-message
32		34
33	.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
34	.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
35	.endif
36
37	CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include" \
38	LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
39	SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \
40	MKDIR="${MKDIR}" RM="${RM}"
41
42	WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
43	EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
44	EMNU_VERSION= 1.0.5
45	HMMER_VERSION= 2.1.1
46	MEME_VERSION= 2.3.1
47	MSE_VERSION= 0.0.4
48	TOPO_VERSION= 0.1
49	PHYLIP_VERSION= 3.573c
50	DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html	35	DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
51	CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template	36	CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template
52		37
53	.for app in EMNU HMMER MEME MSE PHYLIP TOPO
54	SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}"
55	.if defined(WITH_${app})
56	APPLIST+= ${app}
57	${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
58	${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
59	DISTFILES+= ${${app}_DISTFILE}
60	PLIST_${app}= ""
61	.else
62	PLIST_${app}= "@comment "
63	.endif
64	PLIST_SUB+= PLIST_${app}=${PLIST_${app}}
65	.endfor
66
67	# Jemboss support is a work in progress.
68	#
69	#.if defined(WITH_JEMBOSS)
70	#USE_JAVA= 1.3+
71	#CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \
72	# --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L}
73	#CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin
74	#MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin
75	#JEMBOSS_WRKSRC= ${WRKSRC}/jemboss
76	#.endif
77
78	pre-fetch:
79	@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}
80
81	post-extract:
82	.for app in ${APPLIST}
83	@ ${MKDIR} ${EMBASSY_WRKDIR}
84	@ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \
85	${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS}
86	@ if [ `id -u` = 0 ]; then \
87	${CHMOD} -R ug-s ${${app}_WRKSRC}; \
88	${CHOWN} -R 0:0 ${${app}_WRKSRC}; \
89	fi
90	.endfor
91
92	post-patch:	38	post-patch:
		39	.if !defined(NOPORTDOCS)
93	.for DIR in ${DOC_DIRS}	40	.for DIR in ${DOC_DIRS}
94	@ ${PERL} -pi.orig -e \	41	${REINPLACE_CMD} -e \
95	's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \	42	's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
96	${WRKSRC}/${DIR}/Makefile.in	43	${WRKSRC}/${DIR}/Makefile.in
97	.endfor	44	.endfor
98		45	.endif
99	post-configure:
100	.for app in ${APPLIST}
101	@ cd ${${app}_WRKSRC} && \
102	${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \
103	CXXFLAGS="${CXXFLAGS}" \
104	INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \
105	INSTALL_DATA="${INSTALL_DATA}" \
106	INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
107	INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
108	${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
109	.endfor
110
111	post-build:
112	.for app in ${APPLIST}
113	@ cd ${${app}_WRKSRC} && \
114	${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
115	${MAKE_ARGS}
116	.endfor
117	#.if defined(WITH_JEMBOSS)
118	# @ cd ${JEMBOSS_WRKSRC} && \
119	# ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
120	# ${MAKE_ARGS}
121	#.endif
122		46
123	post-install:	47	post-install:
124	.for app in ${APPLIST}	48	@ cd ${WRKSRC} && \
125	@ cd ${${app}_WRKSRC} && \	49	${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
126	${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \	50	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
127	${MAKE_ARGS} ${INSTALL_TARGET}	51	${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
128	.endfor	52	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
129	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
130	${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
131	${CHOWN} ${SHAREOWN}:${SHAREGRP} \
132	${PREFIX}/etc/emboss.default.sample
133	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
134	pkg-message > ${PKGMESSAGE}
135	.if !defined(BATCH)	53	.if !defined(BATCH)
136	@ ${CAT} ${PKGMESSAGE}	54	@ ${CAT} ${PKGMESSAGE}
137	.endif	55	.endif
138
139	post-clean:
140	@ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc
141		56
142	.include <bsd.port.mk>	57	.include <bsd.port.mk>

Lines 1-38 Link Here

(-)emboss/files/patch-emboss-emboss.default.template (-38 lines)
1	--- emboss/emboss.default.template.orig Thu May 24 19:36:39 2001
2	+++ emboss/emboss.default.template Wed May 30 10:23:48 2001
3	@@ -1,9 +1,31 @@
4	-#SET emboss_tempdata name_of_emboss_test_database_directory
5	+#####################################################
6	+### Configuration options for FreeBSD EMBOSS port ###
7	+#####################################################
8
9	-# Logfile - set this to a file that any user can append to
10	-# and EMBOSS applications will automatically write log information
11	+# The directory where EMBOSS expects to find run-time
12	+# databases. This is the compiled-in default - change
13	+# only if you know what you're doing!
14	+#
15	+#SET emboss_data %%PREFIX%%/share/EMBOSS/data
16
17	-#SET emboss_logfile /packages/emboss/emboss/log
18	+# This is an alias which is internal to this
19	+# configuration file and is set here merely as a
20	+# convenience. It points to the location where you
21	+# have placed your local databases (this will differ
22	+# from site to site).
23	+#
24	+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
25	+
26	+# Logfile. If this is uncommented and set to a file
27	+# that any user can append to, EMBOSS applications
28	+# will automatically log usage information.
29	+#
30	+#SET emboss_logfile /var/log/emboss.log
31	+
32	+
33	+###########################################
34	+### Configuration options for databases ###
35	+###########################################
36
37	# swissprot (Puffer fish entries)
38	# =========

Lines 1-73 Link Here

(-)emboss/scripts/configure.emboss (-73 lines)
1	#!/bin/sh
2
3	if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
4	exit
5	fi
6
7	if [ "${BATCH}" ]; then
8	set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\"
9	else
10	/usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
11	--checklist "\n\
12	These third party applications have been adapted to
13	function as part of EMBOSS.\n
14	Please select EMBASSY applications to install:" -1 -1 6 \
15	EMNU "v${EMNU_VERSION} - Text-based menu" ON \
16	HMMER "v${HMMER_VERSION} - HMM alignment" ON \
17	MEME "v${MEME_VERSION} - Motif detection" ON \
18	MSE "v${MSE_VERSION} - Phylogeny inference" ON \
19	PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \
20	TOPO "v${TOPO_VERSION} - Transmembrane display" ON \
21	2> /tmp/checklist.tmp.$$
22
23	retval=$?
24
25	if [ -s /tmp/checklist.tmp.$$ ]; then
26	set `cat /tmp/checklist.tmp.$$`
27	fi
28	${RM} -f /tmp/checklist.tmp.$$
29
30	case $retval in
31	0)
32	if [ -z "$*" ]; then
33	echo "Nothing selected"
34	fi
35	;;
36	1)
37	echo "Cancel pressed."
38	exit 1
39	;;
40	esac
41	fi
42
43	${MKDIR} ${WRKDIRPREFIX}${CURDIR}
44	exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
45
46	while [ "$1" ]; do
47	case $1 in
48	\"EMNU\")
49	echo "WITH_EMNU= yes"
50	;;
51	\"HMMER\")
52	echo "WITH_HMMER= yes"
53	;;
54	\"MEME\")
55	echo "WITH_MEME= yes"
56	;;
57	\"MSE\")
58	echo "WITH_MSE= yes"
59	;;
60	\"PHYLIP\")
61	echo "WITH_PHYLIP= yes"
62	;;
63	\"TOPO\")
64	echo "WITH_TOPO= yes"
65	;;
66	*)
67	echo "Invalid option(s): $*" > /dev/stderr
68	${RM} -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
69	exit 1
70	;;
71	esac
72	shift
73	done

Lines 1-94 Link Here

(-)emboss/pkg-plist (-995 / +1071 lines)
1	%%PLIST_EMNU%%bin/emnu	1	bin/aaindexextract
2	%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
3	%%PLIST_HMMER%%bin/ealistat
4	%%PLIST_HMMER%%bin/ehmmalign
5	%%PLIST_HMMER%%bin/ehmmbuild
6	%%PLIST_HMMER%%bin/ehmmcalibrate
7	%%PLIST_HMMER%%bin/ehmmconvert
8	%%PLIST_HMMER%%bin/ehmmemit
9	%%PLIST_HMMER%%bin/ehmmfetch
10	%%PLIST_HMMER%%bin/ehmmindex
11	%%PLIST_HMMER%%bin/ehmmpfam
12	%%PLIST_HMMER%%bin/ehmmsearch
13	%%PLIST_HMMER%%lib/libhmmer.a
14	%%PLIST_HMMER%%lib/libhmmer.la
15	%%PLIST_HMMER%%lib/libhmmer.so
16	%%PLIST_HMMER%%lib/libhmmer.so.2
17	%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
18	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
19	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
20	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
21	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
22	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
23	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
24	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
25	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
26	%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
27	%%PLIST_MEME%%bin/meme
28	%%PLIST_MEME%%lib/libmeme.a
29	%%PLIST_MEME%%lib/libmeme.la
30	%%PLIST_MEME%%lib/libmeme.so
31	%%PLIST_MEME%%lib/libmeme.so.2
32	%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
33	%%PLIST_MSE%%bin/mse
34	%%PLIST_MSE%%lib/libckit.a
35	%%PLIST_MSE%%lib/libckit.la
36	%%PLIST_MSE%%lib/libckit.so
37	%%PLIST_MSE%%lib/libckit.so.1
38	%%PLIST_MSE%%share/EMBOSS/acd/mse.acd