diff options
| -rw-r--r-- | biology/emboss/Makefile | 10 | ||||
| -rw-r--r-- | biology/emboss/distinfo | 9 | ||||
| -rw-r--r-- | biology/emboss/pkg-descr | 4 | ||||
| -rw-r--r-- | biology/emboss/pkg-plist | 27 | ||||
| -rw-r--r-- | biology/emboss/pkg-plist.EMNU | 2 | ||||
| -rw-r--r-- | biology/emboss/scripts/configure.emboss | 8 |
6 files changed, 47 insertions, 13 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index cf034e5d54f9..23e0b1f66e36 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.8.0 +PORTVERSION= 1.9.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ \ @@ -23,6 +23,7 @@ LIB_DEPENDS= gd.1:${PORTSDIR}/graphics/gd \ USE_GMAKE= yes USE_LIBTOOL= yes USE_XLIB= yes +USE_MOTIF= yes PLIST= ${WRKDIR}/pkg-plist PKGMESSAGE= ${WRKDIR}/pkg-message @@ -31,7 +32,7 @@ PKGMESSAGE= ${WRKDIR}/pkg-message .endif CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include/gd" \ - LIBS="-L${LOCALBASE}/lib" + LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib" SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ MKDIR="${MKDIR}" \ @@ -39,10 +40,11 @@ SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY -PHYLIP_VERSION= 3.573c +EMNU_VERSION= 1.0.2 MSE_VERSION= 0.0.4 TOPO_VERSION= 0.1 -.for app in MSE PHYLIP TOPO +PHYLIP_VERSION= 3.573c +.for app in EMNU 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 1eed31a8b426..fce228f6c4c0 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1,4 +1,5 @@ -MD5 (emboss/EMBOSS-1.8.0.tar.gz) = 4f4b54f5e2c3e053baaffb19f258ad2a -MD5 (emboss/MSE-0.0.4.tar.gz) = 0585be481f33eb71ceadee89b339f86e -MD5 (emboss/PHYLIP-3.573c.tar.gz) = 7186d27d0909ffb5481720ec41d99222 -MD5 (emboss/TOPO-0.1.tar.gz) = a8709a31b1fc2f5914365d87b7120e72 +MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c +MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b +MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f +MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3 +MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29 diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr index 37865f30eebe..1f61ba6fd00a 100644 --- a/biology/emboss/pkg-descr +++ b/biology/emboss/pkg-descr @@ -12,8 +12,8 @@ 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 three currently -available EMBASSY applications - MSE, PHYLIP and TOPO. During an interactive +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 diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index 0c277d0ee003..1cba313f1bd0 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -1,3 +1,4 @@ +bin/abiview bin/acdc bin/antigenic bin/backtranseq @@ -61,6 +62,7 @@ bin/newcpgreport bin/newcpgseek bin/newseq bin/noreturn +bin/notseq bin/nthseq bin/octanol bin/oddcomp @@ -90,8 +92,10 @@ bin/prophet bin/prosextract bin/pscan bin/rebaseextract +bin/recode bin/redata bin/remap +bin/restover bin/restrict bin/revseq bin/seealso @@ -138,6 +142,7 @@ lib/libnucleus.so.1 lib/libplplot.a lib/libplplot.so lib/libplplot.so.4 +share/EMBOSS/acd/abiview.acd share/EMBOSS/acd/ajbad.acd share/EMBOSS/acd/ajfeatest.acd share/EMBOSS/acd/ajtest.acd @@ -215,6 +220,7 @@ share/EMBOSS/acd/newcpgreport.acd share/EMBOSS/acd/newcpgseek.acd share/EMBOSS/acd/newseq.acd share/EMBOSS/acd/noreturn.acd +share/EMBOSS/acd/notseq.acd share/EMBOSS/acd/nthseq.acd share/EMBOSS/acd/octanol.acd share/EMBOSS/acd/oddcomp.acd @@ -247,8 +253,10 @@ share/EMBOSS/acd/prosextract.acd share/EMBOSS/acd/proteinmotifsearch.acd share/EMBOSS/acd/pscan.acd share/EMBOSS/acd/rebaseextract.acd +share/EMBOSS/acd/recode.acd share/EMBOSS/acd/redata.acd share/EMBOSS/acd/remap.acd +share/EMBOSS/acd/restover.acd share/EMBOSS/acd/restrict.acd share/EMBOSS/acd/revseq.acd share/EMBOSS/acd/scope.acd @@ -468,7 +476,11 @@ share/EMBOSS/data/EGC.12 share/EMBOSS/data/EGC.13 share/EMBOSS/data/EGC.14 share/EMBOSS/data/EGC.15 +share/EMBOSS/data/EGC.16 share/EMBOSS/data/EGC.2 +share/EMBOSS/data/EGC.21 +share/EMBOSS/data/EGC.22 +share/EMBOSS/data/EGC.23 share/EMBOSS/data/EGC.3 share/EMBOSS/data/EGC.4 share/EMBOSS/data/EGC.5 @@ -660,11 +672,15 @@ share/doc/EMBOSS/manuals/admin.sty share/doc/EMBOSS/manuals/admin.tex share/doc/EMBOSS/manuals/program.ps.gz share/doc/EMBOSS/programs/html/SITE-DIRECTED.html +share/doc/EMBOSS/programs/html/abi_trace_files_group.html +share/doc/EMBOSS/programs/html/abiview.html +share/doc/EMBOSS/programs/html/abiview0.gif share/doc/EMBOSS/programs/html/alignment_global_group.html share/doc/EMBOSS/programs/html/alignment_group.html share/doc/EMBOSS/programs/html/alignment_local_group.html share/doc/EMBOSS/programs/html/alignment_multiple_group.html share/doc/EMBOSS/programs/html/antigenic.html +share/doc/EMBOSS/programs/html/assorted_group.html share/doc/EMBOSS/programs/html/backtranseq.html share/doc/EMBOSS/programs/html/banana.html share/doc/EMBOSS/programs/html/banana0.gif @@ -743,6 +759,7 @@ share/doc/EMBOSS/programs/html/emboss_icon.gif share/doc/EMBOSS/programs/html/embossdata.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 @@ -783,6 +800,7 @@ share/doc/EMBOSS/programs/html/maskfeat.html share/doc/EMBOSS/programs/html/maskseq.html share/doc/EMBOSS/programs/html/matcher.html share/doc/EMBOSS/programs/html/megamerger.html +share/doc/EMBOSS/programs/html/menus_group.html share/doc/EMBOSS/programs/html/merger.html share/doc/EMBOSS/programs/html/mix.html share/doc/EMBOSS/programs/html/motifs_group.html @@ -796,6 +814,7 @@ share/doc/EMBOSS/programs/html/newcpgreport.html share/doc/EMBOSS/programs/html/newcpgseek.html share/doc/EMBOSS/programs/html/newseq.html share/doc/EMBOSS/programs/html/noreturn.html +share/doc/EMBOSS/programs/html/notseq.html share/doc/EMBOSS/programs/html/nthseq.html share/doc/EMBOSS/programs/html/octanol.html share/doc/EMBOSS/programs/html/octanol0.gif @@ -843,14 +862,15 @@ share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html share/doc/EMBOSS/programs/html/protein_sequence_features_group.html share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html share/doc/EMBOSS/programs/html/pscan.html +share/doc/EMBOSS/programs/html/re_group.html share/doc/EMBOSS/programs/html/rebaseextract.html +share/doc/EMBOSS/programs/html/recode.html share/doc/EMBOSS/programs/html/redata.html share/doc/EMBOSS/programs/html/reformatting_group.html share/doc/EMBOSS/programs/html/remap.html share/doc/EMBOSS/programs/html/repeats_group.html share/doc/EMBOSS/programs/html/restml.html share/doc/EMBOSS/programs/html/restrict.html -share/doc/EMBOSS/programs/html/restriction_enzymes_group.html share/doc/EMBOSS/programs/html/revseq.html share/doc/EMBOSS/programs/html/secondary_structure_group.html share/doc/EMBOSS/programs/html/seealso.html @@ -864,6 +884,7 @@ share/doc/EMBOSS/programs/html/sequence_comparison_group.html share/doc/EMBOSS/programs/html/sequence_composition_group.html share/doc/EMBOSS/programs/html/sequence_display_group.html share/doc/EMBOSS/programs/html/sequence_editing_group.html +share/doc/EMBOSS/programs/html/sequence_features_group.html share/doc/EMBOSS/programs/html/sequence_information_group.html share/doc/EMBOSS/programs/html/showdb.html share/doc/EMBOSS/programs/html/showfeat.html @@ -904,6 +925,7 @@ share/doc/EMBOSS/programs/html/wordcount.html share/doc/EMBOSS/programs/html/wordmatch.html share/doc/EMBOSS/programs/html/wossname.html share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt +share/doc/EMBOSS/programs/text/abiview.txt share/doc/EMBOSS/programs/text/antigenic.txt share/doc/EMBOSS/programs/text/backtranseq.txt share/doc/EMBOSS/programs/text/banana.txt @@ -967,6 +989,7 @@ share/doc/EMBOSS/programs/text/ekitsch.txt share/doc/EMBOSS/programs/text/embossdata.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 @@ -1010,6 +1033,7 @@ share/doc/EMBOSS/programs/text/newcpgreport.txt share/doc/EMBOSS/programs/text/newcpgseek.txt share/doc/EMBOSS/programs/text/newseq.txt share/doc/EMBOSS/programs/text/noreturn.txt +share/doc/EMBOSS/programs/text/notseq.txt share/doc/EMBOSS/programs/text/nthseq.txt share/doc/EMBOSS/programs/text/octanol.txt share/doc/EMBOSS/programs/text/oddcomp.txt @@ -1041,6 +1065,7 @@ 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/recode.txt share/doc/EMBOSS/programs/text/redata.txt share/doc/EMBOSS/programs/text/remap.txt share/doc/EMBOSS/programs/text/restml.txt diff --git a/biology/emboss/pkg-plist.EMNU b/biology/emboss/pkg-plist.EMNU new file mode 100644 index 000000000000..fcb7fe6fe4a6 --- /dev/null +++ b/biology/emboss/pkg-plist.EMNU @@ -0,0 +1,2 @@ +bin/emnu +share/EMBOSS/acd/emnu.acd diff --git a/biology/emboss/scripts/configure.emboss b/biology/emboss/scripts/configure.emboss index a17b495c50b1..b5ad7348def5 100644 --- a/biology/emboss/scripts/configure.emboss +++ b/biology/emboss/scripts/configure.emboss @@ -5,13 +5,14 @@ if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then fi if [ "${BATCH}" ]; then - set \"MSE\" \"PHYLIP\" \"TOPO\" + set \"EMNU\" \"MSE\" \"PHYLIP\" \"TOPO\" else /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \ --checklist "\n\ These third party applications have been adapted to function as part of EMBOSS.\n -Please select EMBASSY applications to install:" -1 -1 3 \ +Please select EMBASSY applications to install:" -1 -1 4 \ +EMNU "v${EMNU_VERSION} - Text-based menu" ON \ MSE "v${MSE_VERSION} - Phylogeny inference" ON \ PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \ TOPO "v${TOPO_VERSION} - Transmembrane display" ON \ @@ -42,6 +43,9 @@ exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc while [ "$1" ]; do case $1 in + \"EMNU\") + echo "WITH_EMNU= yes" + ;; \"MSE\") echo "WITH_MSE= yes" ;; |