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[new port] biology/embassy
PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
This commit is contained in:
Sergey Matveychuk
parent
089dcb9cd7
commit
883e920692
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=122510
@ -18,6 +18,7 @@
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SUBDIR += deft
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SUBDIR += distribfold
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SUBDIR += dna-qc
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SUBDIR += embassy
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SUBDIR += emboss
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SUBDIR += fasta
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SUBDIR += fasta3
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96
biology/embassy/Makefile
Normal file
96
biology/embassy/Makefile
Normal file
@ -0,0 +1,96 @@
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# New ports collection makefile for: embassy
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# Date created: 1.November.2004
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# Whom: Fernan Aguero <fernan@iib.unsamn.edu.ar>
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#
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# $FreeBSD$
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#
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PORTNAME= embassy
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PORTVERSION= 2.9.0
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
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ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
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ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
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DIST_SUBDIR= ${PORTNAME}
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MAINTAINER= fernan@iib.unsam.edu.ar
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COMMENT= A collection of contributed EMBOSS applications
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BUILD_DEPENDS= ${LOCALBASE}/include/emboss.h:${PORTSDIR}/biology/emboss
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LIB_DEPENDS= nucleus.1:${PORTSDIR}/biology/emboss:install
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USE_SUBMAKE= yes
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USE_GMAKE= yes
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GNU_CONFIGURE= yes
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USE_XLIB= yes
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USE_MOTIF= yes
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OPTIONS= DOMAINATRIX "Protein structure and domain apps" on \
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EMNU "EMBOSS simple menu" on \
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ESIM4 "Align cDNA/EST to genome" on \
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HMMER "HMM alignment and searches" on \
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MEME "Motif detection" on \
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MSE "Sequence editor" on \
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PHYLIP "Phylogeny inference" on \
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TOPO "Transmembrane display" on
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CONFIGURE_ENV+= CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \
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LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib"
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EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
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DOMAINATRIX_VERSION= 1.0.0
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EMNU_VERSION= 1.05
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ESIM4_VERSION= 1.0.0
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HMMER_VERSION= 2.1.1
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MEME_VERSION= 2.3.1
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MSE_VERSION= 1.0.0
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TOPO_VERSION= 1.0.0
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PHYLIP_VERSION= 3.57c
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EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO
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.include <bsd.port.pre.mk>
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.for app in ${EMBASSY_APPS}
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.if defined(WITH_${app})
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APPLIST+= ${app}
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${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
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${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
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DISTFILES+= ${${app}_DISTFILE}
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PLIST_${app}= ""
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.else
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PLIST_${app}= "@comment "
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.endif
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PLIST_SUB+= PLIST_${app}=${PLIST_${app}}
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.endfor
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do-extract:
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.for app in ${APPLIST}
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@ ${MKDIR} ${EMBASSY_WRKDIR}
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@ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \
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${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS}
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@ if [ `id -u` = 0 ]; then \
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${CHMOD} -R ug-s ${${app}_WRKSRC}; \
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${CHOWN} -R 0:0 ${${app}_WRKSRC}; \
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fi
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.endfor
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do-configure:
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.for app in ${APPLIST}
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@ cd ${${app}_WRKSRC} && \
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${SETENV} ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
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.endfor
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do-build:
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.for app in ${APPLIST}
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@ cd ${${app}_WRKSRC} && \
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${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS}
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.endfor
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do-install:
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.for app in ${APPLIST}
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@ cd ${${app}_WRKSRC} && \
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${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
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${MAKE_ARGS} ${INSTALL_TARGET}
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.endfor
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.include <bsd.port.post.mk>
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16
biology/embassy/distinfo
Normal file
16
biology/embassy/distinfo
Normal file
@ -0,0 +1,16 @@
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MD5 (embassy/DOMAINATRIX-1.0.0.tar.gz) = 78e1145851073a277e568ee3a691d999
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SIZE (embassy/DOMAINATRIX-1.0.0.tar.gz) = 551090
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MD5 (embassy/EMNU-1.05.tar.gz) = b091db115506ef89157b1cfb92a964b3
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SIZE (embassy/EMNU-1.05.tar.gz) = 341879
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MD5 (embassy/ESIM4-1.0.0.tar.gz) = 3fa1de555365d79bdc38490e09683632
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SIZE (embassy/ESIM4-1.0.0.tar.gz) = 377821
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MD5 (embassy/HMMER-2.1.1.tar.gz) = e7762beca88f2748cb7449e7f89ca068
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SIZE (embassy/HMMER-2.1.1.tar.gz) = 555504
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MD5 (embassy/MEME-2.3.1.tar.gz) = 014237836443382b767efb4b315c2b6d
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SIZE (embassy/MEME-2.3.1.tar.gz) = 417514
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MD5 (embassy/MSE-1.0.0.tar.gz) = f55522c9f474319f56227e6a63c91dad
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SIZE (embassy/MSE-1.0.0.tar.gz) = 407726
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MD5 (embassy/PHYLIP-3.57c.tar.gz) = bd242c3382a82d1a842e0a82778a40c2
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SIZE (embassy/PHYLIP-3.57c.tar.gz) = 856814
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MD5 (embassy/TOPO-1.0.0.tar.gz) = 18409cc3ce6a402690b14a73535ebe07
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SIZE (embassy/TOPO-1.0.0.tar.gz) = 345281
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14
biology/embassy/pkg-descr
Normal file
14
biology/embassy/pkg-descr
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EMBASSY is a collection of contributed EMBOSS software. From the web
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pages:
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"EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL).
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Programs which have been included from third parties who have their own
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licencing terms are kept apart under the EMBASSY grouping.
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This allows the EMBOSS libraries to link to other software, and only
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requires that software to have an LGPL-compatible licence. Phylip, for
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example, fits this model.
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But, to the user they do look exactly like EMBOSS aplications."
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WWW: http://emboss.sourceforge.net/apps/#Embassy
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144
biology/embassy/pkg-plist
Normal file
144
biology/embassy/pkg-plist
Normal file
@ -0,0 +1,144 @@
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%%PLIST_DOMAINATRIX%%bin/contacts
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%%PLIST_DOMAINATRIX%%bin/domainer
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%%PLIST_DOMAINATRIX%%bin/fraggle
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%%PLIST_DOMAINATRIX%%bin/hetparse
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%%PLIST_DOMAINATRIX%%bin/hmmgen
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%%PLIST_DOMAINATRIX%%bin/interface
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%%PLIST_DOMAINATRIX%%bin/libscan
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%%PLIST_DOMAINATRIX%%bin/pdbparse
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%%PLIST_DOMAINATRIX%%bin/pdbplus
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%%PLIST_DOMAINATRIX%%bin/pdbtosp
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%%PLIST_DOMAINATRIX%%bin/profgen
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%%PLIST_DOMAINATRIX%%bin/rocplot
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%%PLIST_DOMAINATRIX%%bin/scopalign
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%%PLIST_DOMAINATRIX%%bin/scopnr
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%%PLIST_DOMAINATRIX%%bin/scopparse
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%%PLIST_DOMAINATRIX%%bin/scoprep
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%%PLIST_DOMAINATRIX%%bin/scopreso
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%%PLIST_DOMAINATRIX%%bin/scopseqs
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%%PLIST_DOMAINATRIX%%bin/seqalign
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%%PLIST_DOMAINATRIX%%bin/seqnr
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%%PLIST_DOMAINATRIX%%bin/seqsearch
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%%PLIST_DOMAINATRIX%%bin/seqsort
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%%PLIST_DOMAINATRIX%%bin/seqwords
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%%PLIST_DOMAINATRIX%%bin/siggen
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%%PLIST_DOMAINATRIX%%bin/sigplot
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%%PLIST_DOMAINATRIX%%bin/sigscan
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%%PLIST_EMNU%%bin/emnu
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%%PLIST_ESIM4%%bin/esim4
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%%PLIST_MEME%%bin/meme
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%%PLIST_HMMER%%bin/ehmmcalibrate
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%%PLIST_HMMER%%bin/ehmmconvert
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%%PLIST_HMMER%%bin/ehmmemit
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%%PLIST_HMMER%%bin/ehmmfetch
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%%PLIST_HMMER%%bin/ehmmindex
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%%PLIST_HMMER%%bin/ehmmbuild
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%%PLIST_HMMER%%bin/ehmmalign
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%%PLIST_HMMER%%bin/ehmmpfam
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%%PLIST_HMMER%%bin/ehmmsearch
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%%PLIST_HMMER%%bin/ealistat
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%%PLIST_MSE%%bin/mse
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%%PLIST_PHYLIP%%bin/eclique
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%%PLIST_PHYLIP%%bin/econsense
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%%PLIST_PHYLIP%%bin/econtml
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%%PLIST_PHYLIP%%bin/econtrast
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%%PLIST_PHYLIP%%bin/ednacomp
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%%PLIST_PHYLIP%%bin/ednadist
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%%PLIST_PHYLIP%%bin/ednainvar
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%%PLIST_PHYLIP%%bin/ednaml
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%%PLIST_PHYLIP%%bin/ednamlk
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%%PLIST_PHYLIP%%bin/ednapars
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%%PLIST_PHYLIP%%bin/ednapenny
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%%PLIST_PHYLIP%%bin/edollop
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%%PLIST_PHYLIP%%bin/edolpenny
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%%PLIST_PHYLIP%%bin/efactor
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%%PLIST_PHYLIP%%bin/efitch
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%%PLIST_PHYLIP%%bin/egendist
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%%PLIST_PHYLIP%%bin/ekitsch
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%%PLIST_PHYLIP%%bin/emix
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%%PLIST_PHYLIP%%bin/epenny
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%%PLIST_PHYLIP%%bin/eprotdist
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%%PLIST_PHYLIP%%bin/eprotpars
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%%PLIST_PHYLIP%%bin/erestml
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%%PLIST_PHYLIP%%bin/eseqboot
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%%PLIST_PHYLIP%%bin/eneighbor
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%%PLIST_TOPO%%bin/topo
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%%PLIST_MEME%%lib/libmeme.so.2
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%%PLIST_MEME%%lib/libmeme.so
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%%PLIST_MEME%%lib/libmeme.la
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%%PLIST_MEME%%lib/libmeme.a
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%%PLIST_HMMER%%lib/libhmmer.so.2
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%%PLIST_HMMER%%lib/libhmmer.so
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%%PLIST_HMMER%%lib/libhmmer.la
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%%PLIST_HMMER%%lib/libhmmer.a
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%%PLIST_MSE%%lib/libckit.so.1
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%%PLIST_MSE%%lib/libckit.so
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%%PLIST_MSE%%lib/libckit.la
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%%PLIST_MSE%%lib/libckit.a
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%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/contacts.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainer.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/fraggle.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hetparse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/hmmgen.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/interface.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/libscan.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbparse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbplus.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/pdbtosp.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/profgen.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/rocplot.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopalign.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopnr.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scoprep.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopreso.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopseqs.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqalign.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqnr.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsearch.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqsort.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/seqwords.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/siggen.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigplot.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/sigscan.acd
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%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
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%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
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%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
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%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
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@dirrm share/EMBOSS/acd
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@dirrm share/EMBOSS
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