From 8784488ca05320f40d19612feaec71dd75d64be8 Mon Sep 17 00:00:00 2001 From: wjv Date: Fri, 3 Aug 2001 11:32:42 +0000 Subject: - Update port to version 2.0.1 - Add two new EMBASSY applications, MEME and HMMER. --- biology/emboss/Makefile | 7 ++- biology/emboss/distinfo | 12 +++-- biology/emboss/pkg-descr | 10 ++-- biology/emboss/pkg-plist | 93 +++++++++++++++++++++++++++++---- biology/emboss/scripts/configure.emboss | 12 ++++- 5 files changed, 110 insertions(+), 24 deletions(-) diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 8d98b41cff6..52c50aea85e 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.13.3 +PORTVERSION= 2.0.1 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ \ @@ -22,6 +22,7 @@ LIB_DEPENDS= gd.2:${PORTSDIR}/graphics/gd USE_GMAKE= yes USE_LIBTOOL= yes +INSTALLS_SHLIB= yes USE_XLIB= yes USE_MOTIF= yes PKGMESSAGE= ${WRKDIR}/pkg-message @@ -38,13 +39,15 @@ SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY EMNU_VERSION= 1.0.4 +HMMER_VERSION= 2.1.1 +MEME_VERSION= 2.3.1 MSE_VERSION= 0.0.4 TOPO_VERSION= 0.1 PHYLIP_VERSION= 3.573c DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template -.for app in EMNU MSE PHYLIP TOPO +.for app in EMNU HMMER MEME MSE PHYLIP TOPO SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" .if defined(WITH_${app}) APPLIST+= ${app} diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index 23a0d3c5749..166c130b027 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1,5 +1,7 @@ -MD5 (emboss/EMBOSS-1.13.3.tar.gz) = ef3ebd34154abf04293f58bd9974267b -MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8 -MD5 (emboss/MSE-0.0.4.tar.gz) = d671afc3a3cc211f038f7752fb09c8f6 -MD5 (emboss/PHYLIP-3.573c.tar.gz) = 3539ae2d0753a6e95e60d59d0177c305 -MD5 (emboss/TOPO-0.1.tar.gz) = 8666694007cf866f5cdfe2aba7c01e3b +MD5 (emboss/EMBOSS-2.0.1.tar.gz) = 7546441cc78be9054c4cdd5e24b97048 +MD5 (emboss/EMNU-1.0.4.tar.gz) = f24a5dcfe2cd7a4423f8dc8ed1946920 +MD5 (emboss/HMMER-2.1.1.tar.gz) = 01686894a1d5ca4b93555648e4e192bd +MD5 (emboss/MEME-2.3.1.tar.gz) = 941921287a49a691d2a78b8726b5ac88 +MD5 (emboss/MSE-0.0.4.tar.gz) = 20661dce0e542b25d17bff86858f6cb2 +MD5 (emboss/PHYLIP-3.573c.tar.gz) = 55c91edc768003f83342f4c8e5b345e4 +MD5 (emboss/TOPO-0.1.tar.gz) = 416f5211bd9a7caee009c743e5a1a268 diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr index 9ab6845287f..2f1998bcc51 100644 --- a/biology/emboss/pkg-descr +++ b/biology/emboss/pkg-descr @@ -13,11 +13,11 @@ core libraries which are under the LGPL. EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. This port includes the currently available -EMBASSY applications - EMNU, MSE, PHYLIP and TOPO. During an interactive -install the user will be asked to choose which of these will be installed -(default: all). Note that the EMBASSY version of PHYLIP should not clash -with the standalone Phylip application due to the fact that its binaries have -been renamed. +EMBASSY applications. During an interactive install the user will be asked +to choose which of these will be installed (default: all). Note that the +EMBASSY versions of PHYLIP and HMMER should not clash with the standalone +versions (also in ports/biology) due to the fact that their binaries have been +renamed. WWW: http://www.emboss.org/ diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index a559dc57ee5..dc31f5f5c51 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -1,5 +1,35 @@ %%PLIST_EMNU%%bin/emnu %%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd +%%PLIST_HMMER%%bin/ealistat +%%PLIST_HMMER%%bin/ehmmalign +%%PLIST_HMMER%%bin/ehmmbuild +%%PLIST_HMMER%%bin/ehmmcalibrate +%%PLIST_HMMER%%bin/ehmmconvert +%%PLIST_HMMER%%bin/ehmmemit +%%PLIST_HMMER%%bin/ehmmfetch +%%PLIST_HMMER%%bin/ehmmindex +%%PLIST_HMMER%%bin/ehmmpfam +%%PLIST_HMMER%%bin/ehmmsearch +%%PLIST_HMMER%%lib/libhmmer.a +%%PLIST_HMMER%%lib/libhmmer.la +%%PLIST_HMMER%%lib/libhmmer.so +%%PLIST_HMMER%%lib/libhmmer.so.2 +%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd +%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd +%%PLIST_MEME%%bin/meme +%%PLIST_MEME%%lib/libmeme.a +%%PLIST_MEME%%lib/libmeme.la +%%PLIST_MEME%%lib/libmeme.so +%%PLIST_MEME%%lib/libmeme.so.2 +%%PLIST_MEME%%share/EMBOSS/acd/meme.acd %%PLIST_MSE%%bin/mse %%PLIST_MSE%%lib/libckit.a %%PLIST_MSE%%lib/libckit.la @@ -72,6 +102,7 @@ bin/codcmp bin/coderet bin/compseq bin/cons +bin/contacts bin/cpgplot bin/cpgreport bin/cusp @@ -113,6 +144,7 @@ bin/getorf bin/helixturnhelix bin/hmoment bin/iep +bin/infoalign bin/infoseq bin/isochore bin/lindna @@ -171,6 +203,7 @@ bin/seealso bin/seqmatchall bin/seqret bin/seqretall +bin/seqretallfeat bin/seqretset bin/seqretsplit bin/showalign @@ -180,11 +213,13 @@ bin/showorf bin/showseq bin/shuffleseq bin/sigcleave +bin/siggen bin/silent bin/splitter bin/stretcher bin/stssearch bin/supermatcher +bin/swissparse bin/syco bin/textsearch bin/tfextract @@ -216,7 +251,6 @@ share/EMBOSS/acd/abiview.acd share/EMBOSS/acd/ajbad.acd share/EMBOSS/acd/ajfeatest.acd share/EMBOSS/acd/ajtest.acd -share/EMBOSS/acd/ajtest2.acd share/EMBOSS/acd/antigenic.acd share/EMBOSS/acd/backtranseq.acd share/EMBOSS/acd/banana.acd @@ -227,7 +261,6 @@ share/EMBOSS/acd/charge.acd share/EMBOSS/acd/checktrans.acd share/EMBOSS/acd/chips.acd share/EMBOSS/acd/cirdna.acd -share/EMBOSS/acd/cluster.acd share/EMBOSS/acd/codcmp.acd share/EMBOSS/acd/coderet.acd share/EMBOSS/acd/codes.english @@ -245,6 +278,7 @@ share/EMBOSS/acd/dbiblast.acd share/EMBOSS/acd/dbifasta.acd share/EMBOSS/acd/dbiflat.acd share/EMBOSS/acd/dbigcg.acd +share/EMBOSS/acd/degapseq.acd share/EMBOSS/acd/demofeatures.acd share/EMBOSS/acd/demolist.acd share/EMBOSS/acd/demosequence.acd @@ -253,6 +287,7 @@ share/EMBOSS/acd/demotable.acd share/EMBOSS/acd/descseq.acd share/EMBOSS/acd/diffseq.acd share/EMBOSS/acd/digest.acd +share/EMBOSS/acd/distmat.acd share/EMBOSS/acd/domainer.acd share/EMBOSS/acd/dotmatcher.acd share/EMBOSS/acd/dotpath.acd @@ -281,6 +316,7 @@ share/EMBOSS/acd/helixturnhelix.acd share/EMBOSS/acd/histogramtest.acd share/EMBOSS/acd/hmoment.acd share/EMBOSS/acd/iep.acd +share/EMBOSS/acd/infoalign.acd share/EMBOSS/acd/infoseq.acd share/EMBOSS/acd/isochore.acd share/EMBOSS/acd/lindna.acd @@ -315,7 +351,6 @@ share/EMBOSS/acd/pepwindow.acd share/EMBOSS/acd/pepwindowall.acd share/EMBOSS/acd/plotcon.acd share/EMBOSS/acd/plotorf.acd -share/EMBOSS/acd/plplottest.acd share/EMBOSS/acd/polydot.acd share/EMBOSS/acd/preg.acd share/EMBOSS/acd/prettyplot.acd @@ -327,8 +362,8 @@ share/EMBOSS/acd/profit.acd share/EMBOSS/acd/prophecy.acd share/EMBOSS/acd/prophet.acd share/EMBOSS/acd/prosextract.acd -share/EMBOSS/acd/proteinmotifsearch.acd share/EMBOSS/acd/pscan.acd +share/EMBOSS/acd/psiblasts.acd share/EMBOSS/acd/rebaseextract.acd share/EMBOSS/acd/recoder.acd share/EMBOSS/acd/redata.acd @@ -336,6 +371,7 @@ share/EMBOSS/acd/remap.acd share/EMBOSS/acd/restover.acd share/EMBOSS/acd/restrict.acd share/EMBOSS/acd/revseq.acd +share/EMBOSS/acd/scopalign.acd share/EMBOSS/acd/scope.acd share/EMBOSS/acd/seealso.acd share/EMBOSS/acd/seqinfo.acd @@ -343,11 +379,9 @@ share/EMBOSS/acd/seqmatchall.acd share/EMBOSS/acd/seqret.acd share/EMBOSS/acd/seqretall.acd share/EMBOSS/acd/seqretallfeat.acd -share/EMBOSS/acd/seqretfeat.acd share/EMBOSS/acd/seqretset.acd share/EMBOSS/acd/seqretsplit.acd share/EMBOSS/acd/seqrettype.acd -share/EMBOSS/acd/seqtofeat.acd share/EMBOSS/acd/showalign.acd share/EMBOSS/acd/showdb.acd share/EMBOSS/acd/showfeat.acd @@ -355,10 +389,10 @@ share/EMBOSS/acd/showorf.acd share/EMBOSS/acd/showseq.acd share/EMBOSS/acd/shuffleseq.acd share/EMBOSS/acd/sigcleave.acd +share/EMBOSS/acd/siggen.acd +share/EMBOSS/acd/sigscan.acd share/EMBOSS/acd/silent.acd -share/EMBOSS/acd/simplesw.acd share/EMBOSS/acd/splitter.acd -share/EMBOSS/acd/stamps.acd share/EMBOSS/acd/stretcher.acd share/EMBOSS/acd/stssearch.acd share/EMBOSS/acd/supermatcher.acd @@ -630,7 +664,11 @@ share/EMBOSS/data/Edna.melt share/EMBOSS/data/Eembl.ior share/EMBOSS/data/Eenergy.dat share/EMBOSS/data/Efeatures.embl +share/EMBOSS/data/Efeatures.emboss share/EMBOSS/data/Efeatures.gff +share/EMBOSS/data/Efeatures.pir +share/EMBOSS/data/Efeatures.protein +share/EMBOSS/data/Efeatures.swiss share/EMBOSS/data/Efreqs.dat share/EMBOSS/data/Ehth.dat share/EMBOSS/data/Ehth87.dat @@ -645,7 +683,11 @@ share/EMBOSS/data/Erna.melt share/EMBOSS/data/Esig.euk share/EMBOSS/data/Esig.pro share/EMBOSS/data/Etags.embl +share/EMBOSS/data/Etags.emboss share/EMBOSS/data/Etags.gff +share/EMBOSS/data/Etags.pir +share/EMBOSS/data/Etags.protein +share/EMBOSS/data/Etags.swiss share/EMBOSS/data/Ewhite-wimley.dat share/EMBOSS/data/PRINTS/dummyfile share/EMBOSS/data/PROSITE/dummyfile @@ -680,6 +722,9 @@ share/EMBOSS/test/data/dna.phylip3 share/EMBOSS/test/data/dna.staden share/EMBOSS/test/data/dna.strider share/EMBOSS/test/data/dna.text +share/EMBOSS/test/data/feat.emft +share/EMBOSS/test/data/feat.fasta +share/EMBOSS/test/data/feat.pir share/EMBOSS/test/data/paamir.pep share/EMBOSS/test/data/prot.acedb share/EMBOSS/test/data/prot.codata @@ -705,10 +750,16 @@ share/EMBOSS/test/embl/est.dat share/EMBOSS/test/embl/fun.dat share/EMBOSS/test/embl/hum1.dat share/EMBOSS/test/embl/inv.dat +share/EMBOSS/test/embl/pln.dat share/EMBOSS/test/embl/pro.dat share/EMBOSS/test/embl/rod.dat +share/EMBOSS/test/embl/sts.dat share/EMBOSS/test/embl/vrl.dat share/EMBOSS/test/embl/vrt.dat +share/EMBOSS/test/pir/acnum.hit +share/EMBOSS/test/pir/acnum.trg +share/EMBOSS/test/pir/division.lkp +share/EMBOSS/test/pir/entrynam.idx share/EMBOSS/test/pir/pir1.header share/EMBOSS/test/pir/pir1.names share/EMBOSS/test/pir/pir1.numbers @@ -789,6 +840,7 @@ share/doc/EMBOSS/programs/html/coderet.html share/doc/EMBOSS/programs/html/compseq.html share/doc/EMBOSS/programs/html/cons.html share/doc/EMBOSS/programs/html/consense.html +share/doc/EMBOSS/programs/html/contacts.html share/doc/EMBOSS/programs/html/contml.html share/doc/EMBOSS/programs/html/contrast.html share/doc/EMBOSS/programs/html/cpgplot.html @@ -844,9 +896,9 @@ share/doc/EMBOSS/programs/html/einverted.html share/doc/EMBOSS/programs/html/ekitsch.html share/doc/EMBOSS/programs/html/emboss_icon.gif share/doc/EMBOSS/programs/html/embossdata.html +share/doc/EMBOSS/programs/html/embossversion.html share/doc/EMBOSS/programs/html/emix.html share/doc/EMBOSS/programs/html/emma.html -share/doc/EMBOSS/programs/html/emnu.html share/doc/EMBOSS/programs/html/emowse.html share/doc/EMBOSS/programs/html/eneighbor.html share/doc/EMBOSS/programs/html/entret.html @@ -878,6 +930,7 @@ share/doc/EMBOSS/programs/html/helixturnhelix.html share/doc/EMBOSS/programs/html/hmoment.html share/doc/EMBOSS/programs/html/iep.html share/doc/EMBOSS/programs/html/index.html +share/doc/EMBOSS/programs/html/infoalign.html share/doc/EMBOSS/programs/html/information_group.html share/doc/EMBOSS/programs/html/infoseq.html share/doc/EMBOSS/programs/html/isochore.html @@ -963,6 +1016,7 @@ share/doc/EMBOSS/programs/html/protein_composition_group.html share/doc/EMBOSS/programs/html/protein_motifs_group.html share/doc/EMBOSS/programs/html/protein_mutation_group.html share/doc/EMBOSS/programs/html/protein_profiles_group.html +share/doc/EMBOSS/programs/html/protein_structure_group.html share/doc/EMBOSS/programs/html/pscan.html share/doc/EMBOSS/programs/html/rebaseextract.html share/doc/EMBOSS/programs/html/recode.html @@ -973,26 +1027,33 @@ share/doc/EMBOSS/programs/html/restml.html share/doc/EMBOSS/programs/html/restover.html share/doc/EMBOSS/programs/html/restrict.html share/doc/EMBOSS/programs/html/revseq.html +share/doc/EMBOSS/programs/html/scopalign.html share/doc/EMBOSS/programs/html/scope.html share/doc/EMBOSS/programs/html/seealso.html share/doc/EMBOSS/programs/html/seqboot.html share/doc/EMBOSS/programs/html/seqmatchall.html share/doc/EMBOSS/programs/html/seqret.html share/doc/EMBOSS/programs/html/seqretall.html +share/doc/EMBOSS/programs/html/seqretallfeat.html share/doc/EMBOSS/programs/html/seqretfeat.html share/doc/EMBOSS/programs/html/seqretset.html share/doc/EMBOSS/programs/html/seqretsplit.html +share/doc/EMBOSS/programs/html/showalign.html share/doc/EMBOSS/programs/html/showdb.html share/doc/EMBOSS/programs/html/showfeat.html share/doc/EMBOSS/programs/html/showorf.html share/doc/EMBOSS/programs/html/showseq.html share/doc/EMBOSS/programs/html/shuffleseq.html share/doc/EMBOSS/programs/html/sigcleave.html +share/doc/EMBOSS/programs/html/siggen.html +share/doc/EMBOSS/programs/html/sigscan.html share/doc/EMBOSS/programs/html/silent.html share/doc/EMBOSS/programs/html/splitter.html +share/doc/EMBOSS/programs/html/stamps.html share/doc/EMBOSS/programs/html/stretcher.html share/doc/EMBOSS/programs/html/stssearch.html share/doc/EMBOSS/programs/html/supermatcher.html +share/doc/EMBOSS/programs/html/swissparse.html share/doc/EMBOSS/programs/html/syco.html share/doc/EMBOSS/programs/html/syco0.gif share/doc/EMBOSS/programs/html/syco1.gif @@ -1036,6 +1097,7 @@ share/doc/EMBOSS/programs/text/complex.txt share/doc/EMBOSS/programs/text/compseq.txt share/doc/EMBOSS/programs/text/cons.txt share/doc/EMBOSS/programs/text/consense.txt +share/doc/EMBOSS/programs/text/contacts.txt share/doc/EMBOSS/programs/text/contml.txt share/doc/EMBOSS/programs/text/contrast.txt share/doc/EMBOSS/programs/text/cpgplot.txt @@ -1085,9 +1147,9 @@ share/doc/EMBOSS/programs/text/egendist.txt share/doc/EMBOSS/programs/text/einverted.txt share/doc/EMBOSS/programs/text/ekitsch.txt share/doc/EMBOSS/programs/text/embossdata.txt +share/doc/EMBOSS/programs/text/embossversion.txt share/doc/EMBOSS/programs/text/emix.txt share/doc/EMBOSS/programs/text/emma.txt -share/doc/EMBOSS/programs/text/emnu.txt share/doc/EMBOSS/programs/text/emowse.txt share/doc/EMBOSS/programs/text/eneighbor.txt share/doc/EMBOSS/programs/text/entret.txt @@ -1114,6 +1176,7 @@ share/doc/EMBOSS/programs/text/getorf.txt share/doc/EMBOSS/programs/text/helixturnhelix.txt share/doc/EMBOSS/programs/text/hmoment.txt share/doc/EMBOSS/programs/text/iep.txt +share/doc/EMBOSS/programs/text/infoalign.txt share/doc/EMBOSS/programs/text/infoseq.txt share/doc/EMBOSS/programs/text/isochore.txt share/doc/EMBOSS/programs/text/kitsch.txt @@ -1174,26 +1237,33 @@ share/doc/EMBOSS/programs/text/restml.txt share/doc/EMBOSS/programs/text/restover.txt share/doc/EMBOSS/programs/text/restrict.txt share/doc/EMBOSS/programs/text/revseq.txt +share/doc/EMBOSS/programs/text/scopalign.txt share/doc/EMBOSS/programs/text/scope.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 +share/doc/EMBOSS/programs/text/seqretallfeat.txt share/doc/EMBOSS/programs/text/seqretfeat.txt share/doc/EMBOSS/programs/text/seqretset.txt share/doc/EMBOSS/programs/text/seqretsplit.txt +share/doc/EMBOSS/programs/text/showalign.txt share/doc/EMBOSS/programs/text/showdb.txt share/doc/EMBOSS/programs/text/showfeat.txt share/doc/EMBOSS/programs/text/showorf.txt share/doc/EMBOSS/programs/text/showseq.txt share/doc/EMBOSS/programs/text/shuffleseq.txt share/doc/EMBOSS/programs/text/sigcleave.txt +share/doc/EMBOSS/programs/text/siggen.txt +share/doc/EMBOSS/programs/text/sigscan.txt share/doc/EMBOSS/programs/text/silent.txt share/doc/EMBOSS/programs/text/splitter.txt +share/doc/EMBOSS/programs/text/stamps.txt share/doc/EMBOSS/programs/text/stretcher.txt share/doc/EMBOSS/programs/text/stssearch.txt share/doc/EMBOSS/programs/text/supermatcher.txt +share/doc/EMBOSS/programs/text/swissparse.txt share/doc/EMBOSS/programs/text/syco.txt share/doc/EMBOSS/programs/text/textsearch.txt share/doc/EMBOSS/programs/text/tfextract.txt @@ -1211,7 +1281,10 @@ share/doc/EMBOSS/programs/text/wordmatch.txt share/doc/EMBOSS/programs/text/wossname.txt share/doc/EMBOSS/tutorials/biblio.bib share/doc/EMBOSS/tutorials/dottup.ps.gz +share/doc/EMBOSS/tutorials/emboss-gcg.ppt +share/doc/EMBOSS/tutorials/emboss-interfaces.ppt share/doc/EMBOSS/tutorials/emboss-talk.ppt +share/doc/EMBOSS/tutorials/emboss_tutorial.ps.gz share/doc/EMBOSS/tutorials/emboss_tutorial.tex share/doc/EMBOSS/tutorials/pepinfo1.ps.gz share/doc/EMBOSS/tutorials/pepinfo2.ps.gz diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss index b5ad7348def..b14bb8e85d8 100644 --- a/biology/emboss/scripts/configure.emboss +++ b/biology/emboss/scripts/configure.emboss @@ -5,14 +5,16 @@ if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then fi if [ "${BATCH}" ]; then - set \"EMNU\" \"MSE\" \"PHYLIP\" \"TOPO\" + set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\" else /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \ --checklist "\n\ These third party applications have been adapted to function as part of EMBOSS.\n -Please select EMBASSY applications to install:" -1 -1 4 \ +Please select EMBASSY applications to install:" -1 -1 6 \ EMNU "v${EMNU_VERSION} - Text-based menu" ON \ +HMMER "v${HMMER_VERSION} - HMM alignment" ON \ +MEME "v${MEME_VERSION} - Motif detection" ON \ MSE "v${MSE_VERSION} - Phylogeny inference" ON \ PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \ TOPO "v${TOPO_VERSION} - Transmembrane display" ON \ @@ -46,6 +48,12 @@ while [ "$1" ]; do \"EMNU\") echo "WITH_EMNU= yes" ;; + \"HMMER\") + echo "WITH_HMMER= yes" + ;; + \"MEME\") + echo "WITH_MEME= yes" + ;; \"MSE\") echo "WITH_MSE= yes" ;; -- cgit