diff options
| -rw-r--r-- | biology/emboss/Makefile | 20 | ||||
| -rw-r--r-- | biology/emboss/distinfo | 2 | ||||
| -rw-r--r-- | biology/emboss/files/patch-aa | 32 | ||||
| -rw-r--r-- | biology/emboss/pkg-plist | 81 |
4 files changed, 83 insertions, 52 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 7264cc695ce4..e246f10d8e31 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.1.0 +PORTVERSION= 1.4.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ DISTNAME= EMBOSS-${PORTVERSION} @@ -22,6 +22,15 @@ USE_LIBTOOL= yes CONFIGURE_ENV= CPPFLAGS="-I${LOCALBASE}/include/gd" \ LIBS="-L${LOCALBASE}/lib" +DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html + +post-patch: +.for DIR in ${DOC_DIRS} + @ ${PERL} -pi.orig -e \ + "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \ + ${WRKSRC}/${DIR}/Makefile.in +.endfor + post-install: @ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \ ${PREFIX}/etc/emboss.default.sample @@ -29,13 +38,4 @@ post-install: @ ${CAT} ${PKGMESSAGE} .endif -DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html - -post-patch: -.for DIR in ${DOC_DIRS} - @perl -pi.orig -e \ - "s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \ - ${WRKSRC}/${DIR}/Makefile.in -.endfor - .include <bsd.port.mk> diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index e9fc3c64e55c..f42c83e49367 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1 +1 @@ -MD5 (EMBOSS-1.1.0.tar.gz) = 9de4ee8a02d397d154cad177b560eaaa +MD5 (EMBOSS-1.4.0.tar.gz) = ba096906cc10d0badbc1c479e61926c9 diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa index 4289821e32b0..f4b1bc46f7a1 100644 --- a/biology/emboss/files/patch-aa +++ b/biology/emboss/files/patch-aa @@ -1,24 +1,26 @@ -Add ${PREFIX}/etc as an acceptable location for emboss.default. (This should -be incorporated into the next version of EMBOSS.) +Add ${PREFIX}/etc as an acceptable location for emboss.default. (I'm still +waiting for this to be incorporated into an official release of EMBOSS.) The port installs ${PREFIX}/etc/emboss.default.sample -- Johann <johann@egenetics.com> ---- ajax/ajnam.c.orig Wed Aug 2 10:18:59 2000 -+++ ajax/ajnam.c Thu Aug 10 10:06:20 2000 -@@ -982,6 +982,13 @@ - prefixRootFile = fopen (ajStrStr(namRootStr), "r"); - } +--- ajax/ajnam.c.orig Thu Aug 17 20:31:30 2000 ++++ ajax/ajnam.c Mon Aug 28 15:12:09 2000 +@@ -984,6 +984,15 @@ + prefixRootFile = fopen (ajStrStr(namRootStr), "r"); + } -+ /* look for $(PREFIX)_ROOT/../emboss.default */ ++ /* look for $(PREFIX)_ROOT/../emboss.default */ + -+ if (!prefixRootFile) { -+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default", prefixRoot, prefix); -+ prefixRootFile = fopen (ajStrStr(namRootStr), "r"); -+ } ++ if (!prefixRootFile) ++ { ++ ajFmtPrintS (&namRootStr, "%s/etc/%s.default", ++ namInstallRoot, prefixCap, prefix); ++ prefixRootFile = fopen (ajStrStr(namRootStr), "r"); ++ } + - if (namFileOrig) - (void) ajStrAppC (&namFileOrig, ", "); - (void) ajStrApp (&namFileOrig, namRootStr); + if (namFileOrig) + (void) ajStrAppC (&namFileOrig, ", "); + (void) ajStrApp (&namFileOrig, namRootStr); diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index dd8d44bd0230..b62a97f96d93 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -19,11 +19,14 @@ bin/dbifasta bin/dbiflat bin/dbigcg bin/descseq +bin/diffseq bin/digest bin/dotmatcher +bin/dotpath bin/dottup bin/dreg bin/einverted +bin/iep bin/embossdata bin/emma bin/equicktandem @@ -39,13 +42,13 @@ bin/garnier bin/geecee bin/getorf bin/helixturnhelix -bin/iep bin/infoseq bin/isochore bin/lindna bin/maskfeat bin/maskseq bin/matcher +bin/megamerger bin/merger bin/msbar bin/needle @@ -73,6 +76,7 @@ bin/preg bin/prettyplot bin/prettyseq bin/prima +bin/primersearch bin/printsextract bin/profit bin/prophecy @@ -96,6 +100,7 @@ bin/showorf bin/showseq bin/shuffleseq bin/sigcleave +bin/silent bin/splitter bin/stretcher bin/stssearch @@ -108,6 +113,7 @@ bin/tfscan bin/tmap bin/transeq bin/trimseq +bin/vectorstrip bin/water bin/wobble bin/wordcount @@ -154,8 +160,10 @@ share/doc/EMBOSS/programs/html/dbifasta.html share/doc/EMBOSS/programs/html/dbigcg.html share/doc/EMBOSS/programs/html/dbiflat.html share/doc/EMBOSS/programs/html/descseq.html +share/doc/EMBOSS/programs/html/diffseq.html share/doc/EMBOSS/programs/html/digest.html share/doc/EMBOSS/programs/html/dotmatcher.html +share/doc/EMBOSS/programs/html/dotpath.html share/doc/EMBOSS/programs/html/dottup.html share/doc/EMBOSS/programs/html/dreg.html share/doc/EMBOSS/programs/html/einverted.html @@ -181,6 +189,7 @@ share/doc/EMBOSS/programs/html/lindna.html 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/merger.html share/doc/EMBOSS/programs/html/msbar.html share/doc/EMBOSS/programs/html/needle.html @@ -208,6 +217,7 @@ share/doc/EMBOSS/programs/html/preg.html share/doc/EMBOSS/programs/html/prettyplot.html share/doc/EMBOSS/programs/html/prettyseq.html share/doc/EMBOSS/programs/html/prima.html +share/doc/EMBOSS/programs/html/primersearch.html share/doc/EMBOSS/programs/html/printsextract.html share/doc/EMBOSS/programs/html/profit.html share/doc/EMBOSS/programs/html/prophecy.html @@ -217,8 +227,8 @@ share/doc/EMBOSS/programs/html/pscan.html share/doc/EMBOSS/programs/html/rebaseextract.html share/doc/EMBOSS/programs/html/redata.html share/doc/EMBOSS/programs/html/remap.html -share/doc/EMBOSS/programs/html/revseq.html share/doc/EMBOSS/programs/html/restrict.html +share/doc/EMBOSS/programs/html/revseq.html share/doc/EMBOSS/programs/html/seealso.html share/doc/EMBOSS/programs/html/seqmatchall.html share/doc/EMBOSS/programs/html/seqret.html @@ -230,6 +240,7 @@ 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/silent.html share/doc/EMBOSS/programs/html/splitter.html share/doc/EMBOSS/programs/html/stretcher.html share/doc/EMBOSS/programs/html/stssearch.html @@ -242,6 +253,7 @@ share/doc/EMBOSS/programs/html/tfscan.html share/doc/EMBOSS/programs/html/tmap.html share/doc/EMBOSS/programs/html/transeq.html share/doc/EMBOSS/programs/html/trimseq.html +share/doc/EMBOSS/programs/html/vectorstrip.html share/doc/EMBOSS/programs/html/water.html share/doc/EMBOSS/programs/html/wobble.html share/doc/EMBOSS/programs/html/wordcount.html @@ -271,8 +283,10 @@ share/doc/EMBOSS/programs/text/dbifasta.txt share/doc/EMBOSS/programs/text/dbiflat.txt share/doc/EMBOSS/programs/text/dbigcg.txt share/doc/EMBOSS/programs/text/descseq.txt +share/doc/EMBOSS/programs/text/diffseq.txt share/doc/EMBOSS/programs/text/digest.txt share/doc/EMBOSS/programs/text/dotmatcher.txt +share/doc/EMBOSS/programs/text/dotpath.txt share/doc/EMBOSS/programs/text/dottup.txt share/doc/EMBOSS/programs/text/dreg.txt share/doc/EMBOSS/programs/text/einverted.txt @@ -293,12 +307,12 @@ share/doc/EMBOSS/programs/text/getorf.txt share/doc/EMBOSS/programs/text/helixturnhelix.txt share/doc/EMBOSS/programs/text/iep.txt share/doc/EMBOSS/programs/text/infoseq.txt -share/doc/EMBOSS/programs/text/tfm.txt share/doc/EMBOSS/programs/text/isochore.txt share/doc/EMBOSS/programs/text/lindna.txt share/doc/EMBOSS/programs/text/maskfeat.txt share/doc/EMBOSS/programs/text/maskseq.txt share/doc/EMBOSS/programs/text/matcher.txt +share/doc/EMBOSS/programs/text/megamerger.txt share/doc/EMBOSS/programs/text/merger.txt share/doc/EMBOSS/programs/text/msbar.txt share/doc/EMBOSS/programs/text/needle.txt @@ -326,6 +340,7 @@ share/doc/EMBOSS/programs/text/preg.txt share/doc/EMBOSS/programs/text/prettyplot.txt share/doc/EMBOSS/programs/text/prettyseq.txt share/doc/EMBOSS/programs/text/prima.txt +share/doc/EMBOSS/programs/text/primersearch.txt share/doc/EMBOSS/programs/text/printsextract.txt share/doc/EMBOSS/programs/text/profit.txt share/doc/EMBOSS/programs/text/prophecy.txt @@ -348,6 +363,7 @@ 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/silent.txt share/doc/EMBOSS/programs/text/splitter.txt share/doc/EMBOSS/programs/text/stretcher.txt share/doc/EMBOSS/programs/text/stssearch.txt @@ -355,10 +371,12 @@ share/doc/EMBOSS/programs/text/supermatcher.txt share/doc/EMBOSS/programs/text/syco.txt share/doc/EMBOSS/programs/text/textsearch.txt 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/transeq.txt share/doc/EMBOSS/programs/text/trimseq.txt +share/doc/EMBOSS/programs/text/vectorstrip.txt share/doc/EMBOSS/programs/text/water.txt share/doc/EMBOSS/programs/text/wobble.txt share/doc/EMBOSS/programs/text/wordcount.txt @@ -370,28 +388,13 @@ share/doc/EMBOSS/tutorials/Makefile.in share/doc/EMBOSS/tutorials/Makefile.in.orig share/EMBOSS/plstnd5.fnt share/EMBOSS/plxtnd5.fnt +share/EMBOSS/acd/Makefile +share/EMBOSS/acd/Makefile.am +share/EMBOSS/acd/Makefile.in share/EMBOSS/acd/ajbad.acd share/EMBOSS/acd/ajfeatest.acd share/EMBOSS/acd/ajtest.acd share/EMBOSS/acd/ajtest2.acd -share/EMBOSS/acd/cluster.acd -share/EMBOSS/acd/demofeatures.acd -share/EMBOSS/acd/demolist.acd -share/EMBOSS/acd/demosequence.acd -share/EMBOSS/acd/demostring.acd -share/EMBOSS/acd/demotable.acd -share/EMBOSS/acd/entrails.acd -share/EMBOSS/acd/histogramtest.acd -share/EMBOSS/acd/patmattest.acd -share/EMBOSS/acd/plplottest.acd -share/EMBOSS/acd/proteinmotifsearch.acd -share/EMBOSS/acd/seqinfo.acd -share/EMBOSS/acd/seqretallfeat.acd -share/EMBOSS/acd/seqretfeat.acd -share/EMBOSS/acd/seqtofeat.acd -share/EMBOSS/acd/simplesw.acd -share/EMBOSS/acd/testplot.acd -share/EMBOSS/acd/treetypedisplay.acd share/EMBOSS/acd/antigenic.acd share/EMBOSS/acd/backtranseq.acd share/EMBOSS/acd/banana.acd @@ -399,7 +402,9 @@ share/EMBOSS/acd/chaos.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/codes.english share/EMBOSS/acd/complex.acd share/EMBOSS/acd/compseq.acd share/EMBOSS/acd/cpgplot.acd @@ -411,17 +416,26 @@ share/EMBOSS/acd/dbiblast.acd share/EMBOSS/acd/dbifasta.acd share/EMBOSS/acd/dbiflat.acd share/EMBOSS/acd/dbigcg.acd +share/EMBOSS/acd/demofeatures.acd +share/EMBOSS/acd/demolist.acd +share/EMBOSS/acd/demosequence.acd +share/EMBOSS/acd/demostring.acd +share/EMBOSS/acd/demotable.acd share/EMBOSS/acd/descseq.acd +share/EMBOSS/acd/diffseq.acd share/EMBOSS/acd/digest.acd -share/EMBOSS/acd/dottup.acd share/EMBOSS/acd/dotmatcher.acd +share/EMBOSS/acd/dotpath.acd +share/EMBOSS/acd/dottup.acd share/EMBOSS/acd/dreg.acd share/EMBOSS/acd/einverted.acd +share/EMBOSS/acd/emboss.default share/EMBOSS/acd/embossdata.acd share/EMBOSS/acd/emma.acd +share/EMBOSS/acd/entrails.acd +share/EMBOSS/acd/etandem.acd share/EMBOSS/acd/equicktandem.acd share/EMBOSS/acd/est2genome.acd -share/EMBOSS/acd/etandem.acd share/EMBOSS/acd/extractseq.acd share/EMBOSS/acd/findkm.acd share/EMBOSS/acd/freak.acd @@ -432,6 +446,7 @@ share/EMBOSS/acd/garnier.acd share/EMBOSS/acd/geecee.acd share/EMBOSS/acd/getorf.acd share/EMBOSS/acd/helixturnhelix.acd +share/EMBOSS/acd/histogramtest.acd share/EMBOSS/acd/iep.acd share/EMBOSS/acd/infoseq.acd share/EMBOSS/acd/isochore.acd @@ -439,6 +454,7 @@ share/EMBOSS/acd/lindna.acd share/EMBOSS/acd/maskfeat.acd share/EMBOSS/acd/maskseq.acd share/EMBOSS/acd/matcher.acd +share/EMBOSS/acd/megamerger.acd share/EMBOSS/acd/merger.acd share/EMBOSS/acd/msbar.acd share/EMBOSS/acd/needle.acd @@ -453,60 +469,73 @@ share/EMBOSS/acd/palindrome.acd share/EMBOSS/acd/pasteseq.acd share/EMBOSS/acd/patmatdb.acd share/EMBOSS/acd/patmatmotifs.acd +share/EMBOSS/acd/patmattest.acd share/EMBOSS/acd/pepcoil.acd share/EMBOSS/acd/pepinfo.acd share/EMBOSS/acd/pepnet.acd share/EMBOSS/acd/pepstats.acd share/EMBOSS/acd/pepwheel.acd share/EMBOSS/acd/pepwindow.acd -share/EMBOSS/acd/plotorf.acd share/EMBOSS/acd/pepwindowall.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 share/EMBOSS/acd/prettyseq.acd share/EMBOSS/acd/prima.acd +share/EMBOSS/acd/primersearch.acd share/EMBOSS/acd/printsextract.acd 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/rebaseextract.acd share/EMBOSS/acd/redata.acd share/EMBOSS/acd/remap.acd share/EMBOSS/acd/restrict.acd share/EMBOSS/acd/revseq.acd +share/EMBOSS/acd/seealso.acd +share/EMBOSS/acd/seqinfo.acd 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/showdb.acd share/EMBOSS/acd/showfeat.acd share/EMBOSS/acd/showorf.acd share/EMBOSS/acd/showseq.acd share/EMBOSS/acd/shuffleseq.acd share/EMBOSS/acd/sigcleave.acd +share/EMBOSS/acd/silent.acd +share/EMBOSS/acd/simplesw.acd share/EMBOSS/acd/splitter.acd share/EMBOSS/acd/stretcher.acd share/EMBOSS/acd/stssearch.acd share/EMBOSS/acd/supermatcher.acd share/EMBOSS/acd/syco.acd +share/EMBOSS/acd/testplot.acd +share/EMBOSS/acd/tfm.acd share/EMBOSS/acd/textsearch.acd share/EMBOSS/acd/tfextract.acd -share/EMBOSS/acd/tfm.acd share/EMBOSS/acd/tfscan.acd share/EMBOSS/acd/tmap.acd share/EMBOSS/acd/transeq.acd +share/EMBOSS/acd/treetypedisplay.acd share/EMBOSS/acd/trimseq.acd +share/EMBOSS/acd/vectorstrip.acd share/EMBOSS/acd/water.acd share/EMBOSS/acd/wobble.acd share/EMBOSS/acd/wordcount.acd share/EMBOSS/acd/wordmatch.acd share/EMBOSS/acd/wossname.acd -share/EMBOSS/acd/codes.english share/EMBOSS/data/CODONS/Eacc.cut share/EMBOSS/data/CODONS/Eadenovirus5.cut share/EMBOSS/data/CODONS/Eadenovirus7.cut |