Attachment 48573 Details for Bug 74330 – embassy.shar

embassy.shar

embassy.shar (text/plain), 10.35 KB, created by Fernan Aguero on 2004-11-24 20:00:44 UTC

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Creator: Fernan Aguero

Created: 2004-11-24 20:00:44 UTC

Size: 10.35 KB

patch

obsolete

># This is a shell archive.  Save it in a file, remove anything before
># this line, and then unpack it by entering "sh file".  Note, it may
># create directories; files and directories will be owned by you and
># have default permissions.
>#
># This archive contains:
>#
>#	embassy
>#	embassy/Makefile
>#	embassy/distinfo
>#	embassy/pkg-descr
>#	embassy/pkg-plist
>#
>echo c - embassy
>mkdir -p embassy > /dev/null 2>&1
>echo x - embassy/Makefile
>sed 's/^X//' >embassy/Makefile << 'END-of-embassy/Makefile'
>X# New ports collection makefile for:	embassy
>X# Date created:		1.November.2004
>X# Whom:	      		Fernan Aguero <fernan@iib.unsamn.edu.ar>
>X#
>X# $FreeBSD$
>X#
>X
>XPORTNAME=	embassy
>XPORTVERSION=	2.9.0
>XCATEGORIES=	biology
>XMASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
>X		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
>X		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
>XDIST_SUBDIR=	${PORTNAME}
>X
>XMAINTAINER=	fernan@iib.unsam.edu.ar
>XCOMMENT=	A collection of contributed EMBOSS applications
>X
>XBUILD_DEPENDS=	${LOCALBASE}/include/emboss.h:${PORTSDIR}/biology/emboss
>XLIB_DEPENDS=	nucleus.1:${PORTSDIR}/biology/emboss:install
>X
>XUSE_SUBMAKE=	yes
>XUSE_GMAKE=	yes
>XGNU_CONFIGURE=	yes
>XUSE_XLIB=	yes
>XUSE_MOTIF=	yes
>X
>XOPTIONS=	DOMAINATRIX	"Protein structure and domain apps" on \
>X		EMNU		"EMBOSS simple menu" on \
>X		ESIM4		"Align cDNA/EST to genome" on \
>X		HMMER		"HMM alignment and searches" on \
>X		MEME		"Motif detection" on \
>X		MSE		"Sequence editor" on \
>X		PHYLIP		"Phylogeny inference" on \
>X		TOPO		"Transmembrane display" on
>X
>XCONFIGURE_ENV+=	CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
>X		LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
>X
>XEMBASSY_WRKDIR=		${WRKSRC}/EMBASSY
>XDOMAINATRIX_VERSION=	1.0.0
>XEMNU_VERSION=		1.05
>XESIM4_VERSION=		1.0.0
>XHMMER_VERSION=		2.1.1
>XMEME_VERSION=		2.3.1
>XMSE_VERSION=		1.0.0
>XTOPO_VERSION=		1.0.0
>XPHYLIP_VERSION=		3.57c
>XEMBASSY_APPS=		DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO
>X
>X.include <bsd.port.pre.mk>
>X
>X.for app in ${EMBASSY_APPS}
>X.if defined(WITH_${app})
>XAPPLIST+=	${app}
>X${app}_WRKSRC=	${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
>X${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
>XDISTFILES+=	${${app}_DISTFILE}
>XPLIST_${app}=	""
>X.else
>XPLIST_${app}=	"@comment "
>X.endif
>XPLIST_SUB+=	PLIST_${app}=${PLIST_${app}}
>X.endfor
>X
>Xdo-extract:
>X.for app in ${APPLIST}
>X	@ ${MKDIR} ${EMBASSY_WRKDIR}
>X	@ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \
>X	  ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS}
>X	@ if [ `id -u` = 0 ]; then \
>X	    ${CHMOD} -R ug-s ${${app}_WRKSRC}; \
>X	    ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \
>X	  fi
>X.endfor
>X
>Xdo-configure:
>X.for app in ${APPLIST}
>X	@ cd ${${app}_WRKSRC} && \
>X	  ${SETENV} ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
>X.endfor
>X
>Xdo-build:
>X.for app in ${APPLIST}
>X	@ cd ${${app}_WRKSRC} && \
>X	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS}
>X.endfor
>X
>Xdo-install:
>X.for app in ${APPLIST}
>X	@ cd ${${app}_WRKSRC} && \
>X	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
>X	  ${MAKE_ARGS} ${INSTALL_TARGET}
>X.endfor
>X
>X.include <bsd.port.post.mk>
>END-of-embassy/Makefile
>echo x - embassy/distinfo
>sed 's/^X//' >embassy/distinfo << 'END-of-embassy/distinfo'
>XMD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 78e1145851073a277e568ee3a691d999
>XMD5 (embassy/EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472
>XMD5 (embassy/EMNU-1.05.tar.gz) = 81435e71026a8ae6c361831a38ec1662
>XMD5 (embassy/ESIM4-1.0.0.tar.gz) = d00209b958a45a1ba7cb617950e3fa48
>XMD5 (embassy/HMMER-2.1.1.tar.gz) = e060f31a25074dd64a7885a85cbc15da
>XMD5 (embassy/MEME-2.3.1.tar.gz) = f81f0a6fffcd202e577b25085037bb5e
>XMD5 (embassy/MSE-1.0.0.tar.gz) = c599e848a44d6353e42fb59578417e41
>XMD5 (embassy/PHYLIP-3.57c.tar.gz) = 7ded34afbb6745e0030bfff098f6a674
>XMD5 (embassy/TOPO-1.0.0.tar.gz) = 51885b65b79b87631f3536362e453ed8
>XSIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 551090
>XSIZE (embassy/EMNU-1.05.tar.gz) = 340031
>XSIZE (embassy/ESIM4-1.0.0.tar.gz) = 375473
>XSIZE (embassy/HMMER-2.1.1.tar.gz) = 552322
>XSIZE (embassy/MEME-2.3.1.tar.gz) = 415122
>XSIZE (embassy/MSE-1.0.0.tar.gz) = 405440
>XSIZE (embassy/PHYLIP-3.57c.tar.gz) = 851589
>XSIZE (embassy/TOPO-1.0.0.tar.gz) = 342704
>END-of-embassy/distinfo
>echo x - embassy/pkg-descr
>sed 's/^X//' >embassy/pkg-descr << 'END-of-embassy/pkg-descr'
>XEMBASSY is a collection of contributed EMBOSS software. From the web
>Xpages:
>X
>X "EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL).
>X Programs which have been included from third parties who have their own
>X licencing terms are kept apart under the EMBASSY grouping.
>X
>X This allows the EMBOSS libraries to link to other software, and only
>X requires that software to have an LGPL-compatible licence. Phylip, for
>X example, fits this model.
>X
>X But, to the user they do look exactly like EMBOSS aplications."
>X
>XWWW: http://emboss.sourceforge.net/apps/#Embassy
>END-of-embassy/pkg-descr
>echo x - embassy/pkg-plist
>sed 's/^X//' >embassy/pkg-plist << 'END-of-embassy/pkg-plist'
>X%%PLIST_DOMAINATRIX%%bin/contacts
>X%%PLIST_DOMAINATRIX%%bin/domainer
>X%%PLIST_DOMAINATRIX%%bin/fraggle
>X%%PLIST_DOMAINATRIX%%bin/hetparse
>X%%PLIST_DOMAINATRIX%%bin/hmmgen
>X%%PLIST_DOMAINATRIX%%bin/interface
>X%%PLIST_DOMAINATRIX%%bin/libscan
>X%%PLIST_DOMAINATRIX%%bin/pdbparse
>X%%PLIST_DOMAINATRIX%%bin/pdbplus
>X%%PLIST_DOMAINATRIX%%bin/pdbtosp
>X%%PLIST_DOMAINATRIX%%bin/profgen
>X%%PLIST_DOMAINATRIX%%bin/rocplot
>X%%PLIST_DOMAINATRIX%%bin/scopalign
>X%%PLIST_DOMAINATRIX%%bin/scopnr
>X%%PLIST_DOMAINATRIX%%bin/scopparse
>X%%PLIST_DOMAINATRIX%%bin/scoprep
>X%%PLIST_DOMAINATRIX%%bin/scopreso
>X%%PLIST_DOMAINATRIX%%bin/scopseqs
>X%%PLIST_DOMAINATRIX%%bin/seqalign
>X%%PLIST_DOMAINATRIX%%bin/seqnr
>X%%PLIST_DOMAINATRIX%%bin/seqsearch
>X%%PLIST_DOMAINATRIX%%bin/seqsort
>X%%PLIST_DOMAINATRIX%%bin/seqwords
>X%%PLIST_DOMAINATRIX%%bin/siggen
>X%%PLIST_DOMAINATRIX%%bin/sigplot
>X%%PLIST_DOMAINATRIX%%bin/sigscan
>X%%PLIST_EMNU%%bin/emnu
>X%%PLIST_ESIM4%%bin/esim4
>X%%PLIST_MEME%%bin/meme
>X%%PLIST_HMMER%%bin/ehmmcalibrate
>X%%PLIST_HMMER%%bin/ehmmconvert
>X%%PLIST_HMMER%%bin/ehmmemit
>X%%PLIST_HMMER%%bin/ehmmfetch
>X%%PLIST_HMMER%%bin/ehmmindex
>X%%PLIST_HMMER%%bin/ehmmbuild
>X%%PLIST_HMMER%%bin/ehmmalign
>X%%PLIST_HMMER%%bin/ehmmpfam
>X%%PLIST_HMMER%%bin/ehmmsearch
>X%%PLIST_HMMER%%bin/ealistat
>X%%PLIST_MSE%%bin/mse
>X%%PLIST_PHYLIP%%bin/eclique
>X%%PLIST_PHYLIP%%bin/econsense
>X%%PLIST_PHYLIP%%bin/econtml
>X%%PLIST_PHYLIP%%bin/econtrast
>X%%PLIST_PHYLIP%%bin/ednacomp
>X%%PLIST_PHYLIP%%bin/ednadist
>X%%PLIST_PHYLIP%%bin/ednainvar
>X%%PLIST_PHYLIP%%bin/ednaml
>X%%PLIST_PHYLIP%%bin/ednamlk
>X%%PLIST_PHYLIP%%bin/ednapars
>X%%PLIST_PHYLIP%%bin/ednapenny
>X%%PLIST_PHYLIP%%bin/edollop
>X%%PLIST_PHYLIP%%bin/edolpenny
>X%%PLIST_PHYLIP%%bin/efactor
>X%%PLIST_PHYLIP%%bin/efitch
>X%%PLIST_PHYLIP%%bin/egendist
>X%%PLIST_PHYLIP%%bin/ekitsch
>X%%PLIST_PHYLIP%%bin/emix
>X%%PLIST_PHYLIP%%bin/epenny
>X%%PLIST_PHYLIP%%bin/eprotdist
>X%%PLIST_PHYLIP%%bin/eprotpars
>X%%PLIST_PHYLIP%%bin/erestml
>X%%PLIST_PHYLIP%%bin/eseqboot
>X%%PLIST_PHYLIP%%bin/eneighbor
>X%%PLIST_TOPO%%bin/topo
>X%%PLIST_MEME%%lib/libmeme.so.2
>X%%PLIST_MEME%%lib/libmeme.so
>X%%PLIST_MEME%%lib/libmeme.la
>X%%PLIST_MEME%%lib/libmeme.a
>X%%PLIST_HMMER%%lib/libhmmer.so.2
>X%%PLIST_HMMER%%lib/libhmmer.so
>X%%PLIST_HMMER%%lib/libhmmer.la
>X%%PLIST_HMMER%%lib/libhmmer.a
>X%%PLIST_MSE%%lib/libckit.so.1
>X%%PLIST_MSE%%lib/libckit.so
>X%%PLIST_MSE%%lib/libckit.la
>X%%PLIST_MSE%%lib/libckit.a
>X%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/contacts.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainer.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/fraggle.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hetparse.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hmmgen.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/interface.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/libscan.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbparse.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbplus.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbtosp.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/profgen.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocplot.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopalign.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopnr.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scoprep.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopreso.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopseqs.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqalign.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqnr.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsearch.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsort.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqwords.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/siggen.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigplot.acd
>X%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigscan.acd
>X%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
>X%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
>X%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
>X%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
>X%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
>X%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
>END-of-embassy/pkg-plist
>exit

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Attachments on bug 74330: 48573 | 48574