- Update port biology/emboss from 1.7.0 to 1.8.0
PR: 23130 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
This commit is contained in:
James E. Housley
parent
6f7fe637e3
commit
c318e4acb5
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=35477
@ -6,14 +6,13 @@
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#
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PORTNAME= emboss
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PORTVERSION= 1.7.0
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PORTREVISION= 1
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PORTVERSION= 1.8.0
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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.no.embnet.org/pub/EMBOSS/
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DISTFILES= ${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX}
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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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EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
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MAINTAINER= johann@egenetics.com
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@ -24,9 +23,7 @@ USE_GMAKE= yes
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USE_LIBTOOL= yes
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USE_XLIB= yes
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PLIST= ${WRKDIR}/pkg-plist
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# Make doesn't know about :U
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PORTNAME_U= EMBOSS
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PKGMESSAGE= ${WRKDIR}/pkg-message
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.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
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.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc"
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@ -39,7 +36,7 @@ SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \
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MKDIR="${MKDIR}" \
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RM="${RM}"
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WRKSRC= ${WRKDIR}/${PORTNAME_U}-${PORTVERSION}
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WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
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EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
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PHYLIP_VERSION= 3.573c
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MSE_VERSION= 0.0.4
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@ -109,6 +106,8 @@ post-install:
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@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
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${PREFIX}/etc/emboss.default.sample
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.if !defined(BATCH)
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@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
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pkg-message > ${PKGMESSAGE}
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@ ${CAT} ${PKGMESSAGE}
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.endif
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@ -1,4 +1,4 @@
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MD5 (emboss/EMBOSS-1.7.0.tar.gz) = 61758add8d2d6bdb9e043fe93c37f341
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = e41b0552196e9b7b46ca0e9563e9384a
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MD5 (emboss/MSE-0.0.4.tar.gz) = 6ba124ff85465be3541d2e250248cd3d
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MD5 (emboss/TOPO-0.1.tar.gz) = 687c6ca8ba945520b11058ba28ee880d
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MD5 (emboss/EMBOSS-1.8.0.tar.gz) = 4cbc80557dbbe41fbedb477e00e47aba
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MD5 (emboss/MSE-0.0.4.tar.gz) = 800216297fa6c3de76f6d1d7ea194a22
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = bd2ded015838da4236c3d4ac25ae8ede
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MD5 (emboss/TOPO-0.1.tar.gz) = 42f4f6e57e4c99b4684b0a4810f2c0a0
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@ -3,13 +3,12 @@
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The EMBOSS suite has been successfully installed.
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In order to use the EMBOSS programs, you will need to set some environment
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variables in your shell startup file. If EMBOSS was installed to the
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default prefix, then:
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variables in your shell startup file.
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- set PLPLOT_LIB to: "/usr/local/share/EMBOSS"
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- set EMBOSS_ACDROOT to: "/usr/local/share/EMBOSS/acd"
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- set PLPLOT_LIB to: "%%PREFIX%%/share/EMBOSS"
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- set EMBOSS_ACDROOT to: "%%PREFIX%%/share/EMBOSS/acd"
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NB: A sample configuration file has been installed to /usr/local/etc as
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NB: A sample configuration file has been installed to %%PREFIX%%/etc as
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emboss.default.sample. This must be renamed to emboss.default and edited
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to suit your site and its requirements.
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@ -8,6 +8,7 @@ bin/checktrans
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bin/chips
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bin/cirdna
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bin/codcmp
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bin/coderet
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bin/complex
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bin/compseq
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bin/cons
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@ -151,10 +152,12 @@ share/EMBOSS/acd/chips.acd
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share/EMBOSS/acd/cirdna.acd
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share/EMBOSS/acd/cluster.acd
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share/EMBOSS/acd/codcmp.acd
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share/EMBOSS/acd/coderet.acd
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share/EMBOSS/acd/codes.english
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share/EMBOSS/acd/complex.acd
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share/EMBOSS/acd/compseq.acd
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share/EMBOSS/acd/cons.acd
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share/EMBOSS/acd/corbatest.acd
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share/EMBOSS/acd/cpgplot.acd
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share/EMBOSS/acd/cpgreport.acd
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share/EMBOSS/acd/cusp.acd
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@ -248,6 +251,7 @@ share/EMBOSS/acd/redata.acd
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share/EMBOSS/acd/remap.acd
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share/EMBOSS/acd/restrict.acd
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share/EMBOSS/acd/revseq.acd
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share/EMBOSS/acd/scope.acd
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share/EMBOSS/acd/seealso.acd
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share/EMBOSS/acd/seqinfo.acd
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share/EMBOSS/acd/seqmatchall.acd
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@ -532,16 +536,20 @@ share/EMBOSS/data/Eantigenic.dat
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share/EMBOSS/data/Ebases.iub
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share/EMBOSS/data/Edayhoff.freq
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share/EMBOSS/data/Edna.melt
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share/EMBOSS/data/Eembl.ior
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share/EMBOSS/data/Eenergy.dat
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share/EMBOSS/data/Efeatures.embl
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share/EMBOSS/data/Efeatures.gff
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share/EMBOSS/data/Efreqs.dat
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share/EMBOSS/data/Ehth.dat
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share/EMBOSS/data/Ehth87.dat
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share/EMBOSS/data/Ememe.dat
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share/EMBOSS/data/Enakai.dat
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share/EMBOSS/data/Epepcoil.dat
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share/EMBOSS/data/Epk.dat
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share/EMBOSS/data/Epprofile
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share/EMBOSS/data/Eprior1.plib
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share/EMBOSS/data/Eprior30.plib
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share/EMBOSS/data/Erna.melt
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share/EMBOSS/data/Esig.euk
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share/EMBOSS/data/Esig.pro
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@ -666,12 +674,17 @@ share/doc/EMBOSS/programs/html/chaos0.gif
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share/doc/EMBOSS/programs/html/checktrans.html
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share/doc/EMBOSS/programs/html/chips.html
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share/doc/EMBOSS/programs/html/cirdna.html
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share/doc/EMBOSS/programs/html/clique.html
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share/doc/EMBOSS/programs/html/codcmp.html
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share/doc/EMBOSS/programs/html/coderet.html
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share/doc/EMBOSS/programs/html/coding_regions_group.html
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share/doc/EMBOSS/programs/html/comparison_group.html
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share/doc/EMBOSS/programs/html/complex.html
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share/doc/EMBOSS/programs/html/compseq.html
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share/doc/EMBOSS/programs/html/cons.html
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share/doc/EMBOSS/programs/html/consense.html
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share/doc/EMBOSS/programs/html/contml.html
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share/doc/EMBOSS/programs/html/contrast.html
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share/doc/EMBOSS/programs/html/cpg_islands_group.html
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share/doc/EMBOSS/programs/html/cpgplot.html
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share/doc/EMBOSS/programs/html/cpgplot0.gif
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@ -693,31 +706,67 @@ share/doc/EMBOSS/programs/html/display_alignment_multiple_group.html
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share/doc/EMBOSS/programs/html/dna_sequence_composition_group.html
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share/doc/EMBOSS/programs/html/dna_sequence_features_group.html
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share/doc/EMBOSS/programs/html/dna_sequence_properties_group.html
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share/doc/EMBOSS/programs/html/dnacomp.html
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share/doc/EMBOSS/programs/html/dnadist.html
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share/doc/EMBOSS/programs/html/dnainvar.html
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share/doc/EMBOSS/programs/html/dnaml.html
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share/doc/EMBOSS/programs/html/dnamlk.html
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share/doc/EMBOSS/programs/html/dnapars.html
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share/doc/EMBOSS/programs/html/dnapenny.html
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share/doc/EMBOSS/programs/html/dollop.html
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share/doc/EMBOSS/programs/html/dolpenny.html
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share/doc/EMBOSS/programs/html/dotmatcher.html
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share/doc/EMBOSS/programs/html/dotmatcher0.gif
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share/doc/EMBOSS/programs/html/dotpath.html
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share/doc/EMBOSS/programs/html/dottup.html
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share/doc/EMBOSS/programs/html/dottup0.gif
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share/doc/EMBOSS/programs/html/dreg.html
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share/doc/EMBOSS/programs/html/eclique.html
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share/doc/EMBOSS/programs/html/econsense.html
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share/doc/EMBOSS/programs/html/econtml.html
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share/doc/EMBOSS/programs/html/econtrast.html
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share/doc/EMBOSS/programs/html/ednacomp.html
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share/doc/EMBOSS/programs/html/ednadist.html
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share/doc/EMBOSS/programs/html/ednainvar.html
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share/doc/EMBOSS/programs/html/ednaml.html
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share/doc/EMBOSS/programs/html/ednamlk.html
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share/doc/EMBOSS/programs/html/ednapars.html
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share/doc/EMBOSS/programs/html/ednapenny.html
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share/doc/EMBOSS/programs/html/edollop.html
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share/doc/EMBOSS/programs/html/edolpenny.html
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share/doc/EMBOSS/programs/html/efactor.html
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share/doc/EMBOSS/programs/html/efitch.html
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share/doc/EMBOSS/programs/html/egendist.html
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share/doc/EMBOSS/programs/html/einverted.html
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share/doc/EMBOSS/programs/html/ekitsch.html
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share/doc/EMBOSS/programs/html/emboss_icon.gif
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share/doc/EMBOSS/programs/html/embossdata.html
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share/doc/EMBOSS/programs/html/emix.html
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share/doc/EMBOSS/programs/html/emma.html
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share/doc/EMBOSS/programs/html/emowse.html
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share/doc/EMBOSS/programs/html/eneighbor.html
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share/doc/EMBOSS/programs/html/entret.html
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share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
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share/doc/EMBOSS/programs/html/epenny.html
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share/doc/EMBOSS/programs/html/eprotdist.html
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share/doc/EMBOSS/programs/html/eprotpars.html
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share/doc/EMBOSS/programs/html/equicktandem.html
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share/doc/EMBOSS/programs/html/erestml.html
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share/doc/EMBOSS/programs/html/eseqboot.html
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share/doc/EMBOSS/programs/html/est2genome.html
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share/doc/EMBOSS/programs/html/etandem.html
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share/doc/EMBOSS/programs/html/extractseq.html
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share/doc/EMBOSS/programs/html/factor.html
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share/doc/EMBOSS/programs/html/findkm.html
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share/doc/EMBOSS/programs/html/findkm0.gif
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share/doc/EMBOSS/programs/html/fitch.html
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share/doc/EMBOSS/programs/html/freak.html
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share/doc/EMBOSS/programs/html/fuzznuc.html
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share/doc/EMBOSS/programs/html/fuzzpro.html
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share/doc/EMBOSS/programs/html/fuzztran.html
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share/doc/EMBOSS/programs/html/garnier.html
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share/doc/EMBOSS/programs/html/geecee.html
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share/doc/EMBOSS/programs/html/gendist.html
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share/doc/EMBOSS/programs/html/gene_finding_group.html
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share/doc/EMBOSS/programs/html/getorf.html
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share/doc/EMBOSS/programs/html/groups.html
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@ -728,16 +777,20 @@ share/doc/EMBOSS/programs/html/index.html
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share/doc/EMBOSS/programs/html/infoseq.html
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share/doc/EMBOSS/programs/html/isochore.html
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share/doc/EMBOSS/programs/html/isochore0.gif
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share/doc/EMBOSS/programs/html/kitsch.html
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share/doc/EMBOSS/programs/html/lindna.html
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share/doc/EMBOSS/programs/html/maskfeat.html
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share/doc/EMBOSS/programs/html/maskseq.html
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share/doc/EMBOSS/programs/html/matcher.html
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share/doc/EMBOSS/programs/html/megamerger.html
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share/doc/EMBOSS/programs/html/merger.html
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share/doc/EMBOSS/programs/html/mix.html
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share/doc/EMBOSS/programs/html/motifs_group.html
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share/doc/EMBOSS/programs/html/msbar.html
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share/doc/EMBOSS/programs/html/mse.html
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share/doc/EMBOSS/programs/html/mutation_group.html
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share/doc/EMBOSS/programs/html/needle.html
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share/doc/EMBOSS/programs/html/neighbor.html
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share/doc/EMBOSS/programs/html/new_group_group.html
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share/doc/EMBOSS/programs/html/newcpgreport.html
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share/doc/EMBOSS/programs/html/newcpgseek.html
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@ -752,6 +805,7 @@ share/doc/EMBOSS/programs/html/pasteseq.html
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share/doc/EMBOSS/programs/html/patmatdb.html
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share/doc/EMBOSS/programs/html/patmatmotifs.html
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share/doc/EMBOSS/programs/html/pattern_matching_group.html
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share/doc/EMBOSS/programs/html/penny.html
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share/doc/EMBOSS/programs/html/pepcoil.html
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share/doc/EMBOSS/programs/html/pepinfo.html
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share/doc/EMBOSS/programs/html/pepinfo1.gif
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@ -784,6 +838,7 @@ share/doc/EMBOSS/programs/html/profit.html
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share/doc/EMBOSS/programs/html/prophecy.html
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share/doc/EMBOSS/programs/html/prophet.html
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share/doc/EMBOSS/programs/html/prosextract.html
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share/doc/EMBOSS/programs/html/protdist.html
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share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html
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share/doc/EMBOSS/programs/html/protein_sequence_features_group.html
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share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html
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@ -793,11 +848,13 @@ share/doc/EMBOSS/programs/html/redata.html
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share/doc/EMBOSS/programs/html/reformatting_group.html
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share/doc/EMBOSS/programs/html/remap.html
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share/doc/EMBOSS/programs/html/repeats_group.html
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share/doc/EMBOSS/programs/html/restml.html
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share/doc/EMBOSS/programs/html/restrict.html
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share/doc/EMBOSS/programs/html/restriction_enzymes_group.html
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share/doc/EMBOSS/programs/html/revseq.html
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share/doc/EMBOSS/programs/html/secondary_structure_group.html
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share/doc/EMBOSS/programs/html/seealso.html
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share/doc/EMBOSS/programs/html/seqboot.html
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share/doc/EMBOSS/programs/html/seqmatchall.html
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share/doc/EMBOSS/programs/html/seqret.html
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share/doc/EMBOSS/programs/html/seqretall.html
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@ -830,6 +887,8 @@ share/doc/EMBOSS/programs/html/tfm.html
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share/doc/EMBOSS/programs/html/tfscan.html
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share/doc/EMBOSS/programs/html/tmap.html
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share/doc/EMBOSS/programs/html/tmap0.gif
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share/doc/EMBOSS/programs/html/topo.gif
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share/doc/EMBOSS/programs/html/topo.html
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share/doc/EMBOSS/programs/html/transcription_group.html
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share/doc/EMBOSS/programs/html/transeq.html
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share/doc/EMBOSS/programs/html/translation_group.html
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@ -853,10 +912,15 @@ share/doc/EMBOSS/programs/text/chaos.txt
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share/doc/EMBOSS/programs/text/checktrans.txt
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share/doc/EMBOSS/programs/text/chips.txt
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share/doc/EMBOSS/programs/text/cirdna.txt
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share/doc/EMBOSS/programs/text/clique.txt
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share/doc/EMBOSS/programs/text/codcmp.txt
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share/doc/EMBOSS/programs/text/coderet.txt
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share/doc/EMBOSS/programs/text/complex.txt
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share/doc/EMBOSS/programs/text/compseq.txt
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share/doc/EMBOSS/programs/text/cons.txt
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share/doc/EMBOSS/programs/text/consense.txt
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share/doc/EMBOSS/programs/text/contml.txt
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share/doc/EMBOSS/programs/text/contrast.txt
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share/doc/EMBOSS/programs/text/cpgplot.txt
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share/doc/EMBOSS/programs/text/cpgreport.txt
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share/doc/EMBOSS/programs/text/cusp.txt
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@ -869,39 +933,79 @@ share/doc/EMBOSS/programs/text/dbigcg.txt
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share/doc/EMBOSS/programs/text/descseq.txt
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share/doc/EMBOSS/programs/text/diffseq.txt
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share/doc/EMBOSS/programs/text/digest.txt
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share/doc/EMBOSS/programs/text/dnacomp.txt
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share/doc/EMBOSS/programs/text/dnadist.txt
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share/doc/EMBOSS/programs/text/dnainvar.txt
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share/doc/EMBOSS/programs/text/dnaml.txt
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share/doc/EMBOSS/programs/text/dnamlk.txt
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share/doc/EMBOSS/programs/text/dnapars.txt
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share/doc/EMBOSS/programs/text/dnapenny.txt
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share/doc/EMBOSS/programs/text/dollop.txt
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share/doc/EMBOSS/programs/text/dolpenny.txt
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share/doc/EMBOSS/programs/text/dotmatcher.txt
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share/doc/EMBOSS/programs/text/dotpath.txt
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share/doc/EMBOSS/programs/text/dottup.txt
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share/doc/EMBOSS/programs/text/dreg.txt
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share/doc/EMBOSS/programs/text/eclique.txt
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share/doc/EMBOSS/programs/text/econsense.txt
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share/doc/EMBOSS/programs/text/econtml.txt
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share/doc/EMBOSS/programs/text/econtrast.txt
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share/doc/EMBOSS/programs/text/ednacomp.txt
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share/doc/EMBOSS/programs/text/ednadist.txt
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share/doc/EMBOSS/programs/text/ednainvar.txt
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share/doc/EMBOSS/programs/text/ednaml.txt
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share/doc/EMBOSS/programs/text/ednamlk.txt
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share/doc/EMBOSS/programs/text/ednapars.txt
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share/doc/EMBOSS/programs/text/ednapenny.txt
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share/doc/EMBOSS/programs/text/edollop.txt
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share/doc/EMBOSS/programs/text/edolpenny.txt
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share/doc/EMBOSS/programs/text/efactor.txt
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share/doc/EMBOSS/programs/text/efitch.txt
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share/doc/EMBOSS/programs/text/egendist.txt
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share/doc/EMBOSS/programs/text/einverted.txt
|
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share/doc/EMBOSS/programs/text/ekitsch.txt
|
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share/doc/EMBOSS/programs/text/embossdata.txt
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share/doc/EMBOSS/programs/text/emix.txt
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share/doc/EMBOSS/programs/text/emma.txt
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share/doc/EMBOSS/programs/text/emowse.txt
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share/doc/EMBOSS/programs/text/eneighbor.txt
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share/doc/EMBOSS/programs/text/entret.txt
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share/doc/EMBOSS/programs/text/epenny.txt
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share/doc/EMBOSS/programs/text/eprotdist.txt
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share/doc/EMBOSS/programs/text/eprotpars.txt
|
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share/doc/EMBOSS/programs/text/equicktandem.txt
|
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share/doc/EMBOSS/programs/text/erestml.txt
|
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share/doc/EMBOSS/programs/text/eseqboot.txt
|
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share/doc/EMBOSS/programs/text/est2genome.txt
|
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share/doc/EMBOSS/programs/text/etandem.txt
|
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share/doc/EMBOSS/programs/text/extractseq.txt
|
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share/doc/EMBOSS/programs/text/factor.txt
|
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share/doc/EMBOSS/programs/text/findkm.txt
|
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share/doc/EMBOSS/programs/text/fitch.txt
|
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share/doc/EMBOSS/programs/text/freak.txt
|
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share/doc/EMBOSS/programs/text/fuzznuc.txt
|
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share/doc/EMBOSS/programs/text/fuzzpro.txt
|
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share/doc/EMBOSS/programs/text/fuzztran.txt
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share/doc/EMBOSS/programs/text/garnier.txt
|
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share/doc/EMBOSS/programs/text/geecee.txt
|
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share/doc/EMBOSS/programs/text/gendist.txt
|
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share/doc/EMBOSS/programs/text/getorf.txt
|
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share/doc/EMBOSS/programs/text/helixturnhelix.txt
|
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share/doc/EMBOSS/programs/text/iep.txt
|
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share/doc/EMBOSS/programs/text/infoseq.txt
|
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share/doc/EMBOSS/programs/text/isochore.txt
|
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share/doc/EMBOSS/programs/text/kitsch.txt
|
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share/doc/EMBOSS/programs/text/lindna.txt
|
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share/doc/EMBOSS/programs/text/maskfeat.txt
|
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share/doc/EMBOSS/programs/text/maskseq.txt
|
||||
share/doc/EMBOSS/programs/text/matcher.txt
|
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share/doc/EMBOSS/programs/text/megamerger.txt
|
||||
share/doc/EMBOSS/programs/text/merger.txt
|
||||
share/doc/EMBOSS/programs/text/mix.txt
|
||||
share/doc/EMBOSS/programs/text/msbar.txt
|
||||
share/doc/EMBOSS/programs/text/mse.txt
|
||||
share/doc/EMBOSS/programs/text/needle.txt
|
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share/doc/EMBOSS/programs/text/neighbor.txt
|
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share/doc/EMBOSS/programs/text/newcpgreport.txt
|
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share/doc/EMBOSS/programs/text/newcpgseek.txt
|
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share/doc/EMBOSS/programs/text/newseq.txt
|
||||
@ -913,6 +1017,7 @@ share/doc/EMBOSS/programs/text/palindrome.txt
|
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share/doc/EMBOSS/programs/text/pasteseq.txt
|
||||
share/doc/EMBOSS/programs/text/patmatdb.txt
|
||||
share/doc/EMBOSS/programs/text/patmatmotifs.txt
|
||||
share/doc/EMBOSS/programs/text/penny.txt
|
||||
share/doc/EMBOSS/programs/text/pepcoil.txt
|
||||
share/doc/EMBOSS/programs/text/pepinfo.txt
|
||||
share/doc/EMBOSS/programs/text/pepnet.txt
|
||||
@ -933,13 +1038,16 @@ share/doc/EMBOSS/programs/text/profit.txt
|
||||
share/doc/EMBOSS/programs/text/prophecy.txt
|
||||
share/doc/EMBOSS/programs/text/prophet.txt
|
||||
share/doc/EMBOSS/programs/text/prosextract.txt
|
||||
share/doc/EMBOSS/programs/text/protdist.txt
|
||||
share/doc/EMBOSS/programs/text/pscan.txt
|
||||
share/doc/EMBOSS/programs/text/rebaseextract.txt
|
||||
share/doc/EMBOSS/programs/text/redata.txt
|
||||
share/doc/EMBOSS/programs/text/remap.txt
|
||||
share/doc/EMBOSS/programs/text/restml.txt
|
||||
share/doc/EMBOSS/programs/text/restrict.txt
|
||||
share/doc/EMBOSS/programs/text/revseq.txt
|
||||
share/doc/EMBOSS/programs/text/seealso.txt
|
||||
share/doc/EMBOSS/programs/text/seqboot.txt
|
||||
share/doc/EMBOSS/programs/text/seqmatchall.txt
|
||||
share/doc/EMBOSS/programs/text/seqret.txt
|
||||
share/doc/EMBOSS/programs/text/seqretall.txt
|
||||
@ -962,6 +1070,7 @@ share/doc/EMBOSS/programs/text/tfextract.txt
|
||||
share/doc/EMBOSS/programs/text/tfm.txt
|
||||
share/doc/EMBOSS/programs/text/tfscan.txt
|
||||
share/doc/EMBOSS/programs/text/tmap.txt
|
||||
share/doc/EMBOSS/programs/text/topo.txt
|
||||
share/doc/EMBOSS/programs/text/transeq.txt
|
||||
share/doc/EMBOSS/programs/text/trimseq.txt
|
||||
share/doc/EMBOSS/programs/text/vectorstrip.txt
|
||||
|
||||
Loading…
Reference in New Issue
Block a user