mirror of
https://git.FreeBSD.org/ports.git
synced 2024-12-24 04:33:24 +00:00
- Update to 2.9.0
- Pass maintainership to submitter PR: ports/74333 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
This commit is contained in:
Sergey Matveychuk
parent
6387140db2
commit
626e4b86a8
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=122469
@ -6,137 +6,55 @@
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#
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PORTNAME= emboss
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PORTVERSION= 2.4.1
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PORTREVISION= 3
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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/old/ \
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ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old/
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# ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
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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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DISTNAME= ${PORTNAME:U}-${PORTVERSION}
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DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
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DIST_SUBDIR= ${PORTNAME}
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EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
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MAINTAINER= ports@FreeBSD.org
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MAINTAINER= fernan@iib.unsam.edu.ar
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COMMENT= A collection of open source tools for genetic sequence analysis
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LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd
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BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \
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primer3:${PORTSDIR}/biology/primer3
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LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \
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png.5:${PORTSDIR}/graphics/png
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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_LIBTOOL_VER=15
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INSTALLS_SHLIB= yes
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USE_XLIB= yes
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USE_MOTIF= yes
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USE_PERL5_BUILD=yes
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USE_REINPLACE= yes
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PKGMESSAGE= ${WRKDIR}/pkg-message
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.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
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.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
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.endif
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DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:U}
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DATADIR= ${PREFIX}/share/${PORTNAME:U}
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CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include" \
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LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
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SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \
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MKDIR="${MKDIR}" RM="${RM}"
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WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
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EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
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EMNU_VERSION= 1.0.5
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HMMER_VERSION= 2.1.1
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MEME_VERSION= 2.3.1
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MSE_VERSION= 0.0.4
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TOPO_VERSION= 0.1
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PHYLIP_VERSION= 3.573c
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DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
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CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template
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.for app in EMNU HMMER MEME MSE PHYLIP TOPO
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SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}"
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.if defined(WITH_${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_${app}}
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.endfor
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# Jemboss support is a work in progress.
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#
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#.if defined(WITH_JEMBOSS)
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#USE_JAVA= 1.3+
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#CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \
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# --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L}
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#CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin
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#MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin
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#JEMBOSS_WRKSRC= ${WRKSRC}/jemboss
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#.endif
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pre-fetch:
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@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}
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post-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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post-patch:
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.if !defined(NOPORTDOCS)
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.for DIR in ${DOC_DIRS}
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@ ${PERL} -pi.orig -e \
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's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \
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${REINPLACE_CMD} -e \
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's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
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${WRKSRC}/${DIR}/Makefile.in
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.endfor
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post-configure:
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.for app in ${APPLIST}
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@ cd ${${app}_WRKSRC} && \
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${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \
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CXXFLAGS="${CXXFLAGS}" \
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INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \
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INSTALL_DATA="${INSTALL_DATA}" \
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INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
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INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
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${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
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.endfor
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post-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} ${MAKEFILE} \
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${MAKE_ARGS}
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.endfor
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#.if defined(WITH_JEMBOSS)
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# @ cd ${JEMBOSS_WRKSRC} && \
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# ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
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# ${MAKE_ARGS}
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#.endif
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.endif
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post-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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@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
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${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
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${CHOWN} ${SHAREOWN}:${SHAREGRP} \
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${PREFIX}/etc/emboss.default.sample
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@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
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pkg-message > ${PKGMESSAGE}
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@ cd ${WRKSRC} && \
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${SED} -e 's#%%PREFIX%%#${PREFIX}#' \
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${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
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${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample
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@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
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.if !defined(BATCH)
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@ ${CAT} ${PKGMESSAGE}
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.endif
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post-clean:
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@ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc
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.include <bsd.port.mk>
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@ -1,7 +1,2 @@
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MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad
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MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66
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MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21
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MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c
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MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084
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MD5 (emboss/TOPO-0.1.tar.gz) = a5131f2e0d58e06ce071250b62cbe65a
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MD5 (EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472
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SIZE (EMBOSS-2.9.0.tar.gz) = 14479274
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@ -1,26 +0,0 @@
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Add ${PREFIX}/etc as an acceptable location for emboss.default. (I'm still
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waiting for this to be incorporated into an official release of EMBOSS.)
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The port installs ${PREFIX}/etc/emboss.default.sample
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-- Johann <wjv@FreeBSD.org>
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--- ajax/ajnam.c.orig Thu Aug 17 20:31:30 2000
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+++ ajax/ajnam.c Mon Aug 28 15:12:09 2000
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@@ -984,6 +984,15 @@
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prefixRootFile = fopen (ajStrStr(namRootStr), "r");
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}
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+ /* look for $(PREFIX)_ROOT/../emboss.default */
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+
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+ if (!prefixRootFile)
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+ {
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+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
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+ namInstallRoot, prefix);
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+ prefixRootFile = fopen (ajStrStr(namRootStr), "r");
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+ }
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+
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if (namFileOrig)
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(void) ajStrAppC (&namFileOrig, ", ");
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(void) ajStrApp (&namFileOrig, namRootStr);
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@ -1,11 +0,0 @@
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--- ajax/ajjava.c.orig Thu May 2 22:06:08 2002
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+++ ajax/ajjava.c Sun May 26 09:14:20 2002
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@@ -75,7 +75,7 @@
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#endif
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#ifndef __ppc__
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-#include <crypt.h>
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+#include <unistd.h>
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#endif
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@ -1,11 +0,0 @@
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--- configure.orig Mon Jan 22 23:28:17 2001
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+++ configure Thu Jan 25 19:07:33 2001
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@@ -1473,7 +1473,7 @@
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-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
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+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
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#AC_PROG_CXX
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for ac_prog in mawk gawk nawk awk
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@ -1,38 +0,0 @@
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--- emboss/emboss.default.template.orig Thu May 24 19:36:39 2001
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+++ emboss/emboss.default.template Wed May 30 10:23:48 2001
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@@ -1,9 +1,31 @@
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-#SET emboss_tempdata name_of_emboss_test_database_directory
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+#####################################################
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+### Configuration options for FreeBSD EMBOSS port ###
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+#####################################################
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-# Logfile - set this to a file that any user can append to
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-# and EMBOSS applications will automatically write log information
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+# The directory where EMBOSS expects to find run-time
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+# databases. This is the compiled-in default - change
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+# only if you know what you're doing!
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+#
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+#SET emboss_data %%PREFIX%%/share/EMBOSS/data
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-#SET emboss_logfile /packages/emboss/emboss/log
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+# This is an alias which is internal to this
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+# configuration file and is set here merely as a
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+# convenience. It points to the location where you
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+# have placed your local databases (this will differ
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+# from site to site).
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+#
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+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
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+
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+# Logfile. If this is uncommented and set to a file
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+# that any user can append to, EMBOSS applications
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+# will automatically log usage information.
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+#
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+#SET emboss_logfile /var/log/emboss.log
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+
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+
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+###########################################
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+### Configuration options for databases ###
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+###########################################
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# swissprot (Puffer fish entries)
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# =========
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@ -15,7 +15,8 @@ A .embossrc in a user's home directory overrides settings in the
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system-wide emboss.default.
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Online EMBOSS documentation is available at:
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http://www.uk.embnet.org/Software/EMBOSS/general.html
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http://www.uk.embnet.org/Software/EMBOSS/userdoc.html
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http://www.uk.embnet.org/Software/EMBOSS/Doc/
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http://emboss.sourceforge.net/docs/
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--------------------------------------------------------------------------
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File diff suppressed because it is too large
Load Diff
@ -1,73 +0,0 @@
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#!/bin/sh
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if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then
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exit
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fi
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if [ "${BATCH}" ]; then
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set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\"
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else
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/usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \
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--checklist "\n\
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These third party applications have been adapted to
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function as part of EMBOSS.\n
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Please select EMBASSY applications to install:" -1 -1 6 \
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EMNU "v${EMNU_VERSION} - Text-based menu" ON \
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HMMER "v${HMMER_VERSION} - HMM alignment" ON \
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MEME "v${MEME_VERSION} - Motif detection" ON \
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MSE "v${MSE_VERSION} - Phylogeny inference" ON \
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PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \
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TOPO "v${TOPO_VERSION} - Transmembrane display" ON \
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2> /tmp/checklist.tmp.$$
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retval=$?
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if [ -s /tmp/checklist.tmp.$$ ]; then
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set `cat /tmp/checklist.tmp.$$`
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fi
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${RM} -f /tmp/checklist.tmp.$$
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case $retval in
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0)
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if [ -z "$*" ]; then
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echo "Nothing selected"
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fi
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;;
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1)
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echo "Cancel pressed."
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exit 1
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;;
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esac
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fi
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${MKDIR} ${WRKDIRPREFIX}${CURDIR}
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exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
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while [ "$1" ]; do
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case $1 in
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\"EMNU\")
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echo "WITH_EMNU= yes"
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;;
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\"HMMER\")
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echo "WITH_HMMER= yes"
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;;
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\"MEME\")
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echo "WITH_MEME= yes"
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;;
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\"MSE\")
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echo "WITH_MSE= yes"
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;;
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\"PHYLIP\")
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echo "WITH_PHYLIP= yes"
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;;
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\"TOPO\")
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echo "WITH_TOPO= yes"
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;;
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*)
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echo "Invalid option(s): $*" > /dev/stderr
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${RM} -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc
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exit 1
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;;
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esac
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shift
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done
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Block a user