ports/74330: [new port] biology/embassy
Fernan Aguero
fernan at iib.unsam.edu.ar
Wed Nov 24 20:00:45 UTC 2004
>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 at 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 at 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 at 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:
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