Date: Wed, 24 Nov 2004 16:52:32 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Cc: linimon@FreeBSD.org Subject: ports/74330: [new port] biology/embassy Message-ID: <200411241952.iAOJqWqZ075294@pi.iib.unsam.edu.ar> Resent-Message-ID: <200411242000.iAOK0jWv037890@freefall.freebsd.org>
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>Number: 74330 >Category: ports >Synopsis: [new port] biology/embassy >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Nov 24 20:00:44 GMT 2004 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 4.10-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan@pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386 >Description: The update of the biology/emboss port included the separation of the third-party contributed stuff (called embassy) into its own port. This port was thus part of the emboss Makefile that was rewritten to use the newer OPTIONS. Version has been set to the EMBOSS version, since they are supposed to be in sync. >How-To-Repeat: >Fix: --- embassy.shar begins here --- # 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 --- embassy.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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