diff options
author | nbm <nbm@FreeBSD.org> | 2000-08-13 00:15:48 +0800 |
---|---|---|
committer | nbm <nbm@FreeBSD.org> | 2000-08-13 00:15:48 +0800 |
commit | 854656a18e5b8c10b040fd278aabe87b2367e9de (patch) | |
tree | 5b015dbda855ee879a90e4f0cd1ee158a6ad7178 /biology | |
parent | 7bb720ac3f315679bba10dcf4b67641f2c18a6a1 (diff) | |
download | freebsd-ports-gnome-854656a18e5b8c10b040fd278aabe87b2367e9de.tar.gz freebsd-ports-gnome-854656a18e5b8c10b040fd278aabe87b2367e9de.tar.zst freebsd-ports-gnome-854656a18e5b8c10b040fd278aabe87b2367e9de.zip |
Update to emboss 1.1.0, fixing some style bugs too.
PR: ports/20519
Submitted by: Johann Visagie <johann@egenetics.com> (maintainer)
Diffstat (limited to 'biology')
-rw-r--r-- | biology/emboss/Makefile | 18 | ||||
-rw-r--r-- | biology/emboss/distinfo | 2 | ||||
-rw-r--r-- | biology/emboss/files/patch-aa | 24 | ||||
-rw-r--r-- | biology/emboss/pkg-message | 22 | ||||
-rw-r--r-- | biology/emboss/pkg-plist | 261 |
5 files changed, 321 insertions, 6 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index cc038a5ff719..2279b54b1d9b 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.0.0 +PORTVERSION= 1.1.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ DISTNAME= EMBOSS-${PORTVERSION} @@ -23,4 +23,20 @@ USE_LIBTOOL= yes CONFIGURE_ENV= CPPFLAGS="-I${LOCALBASE}/include/gd" \ LIBS="-L${LOCALBASE}/lib" +post-install: + @ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \ + ${PREFIX}/etc/emboss.default.sample +.if !defined(BATCH) + @ ${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 274c24a97dfa..e9fc3c64e55c 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1 +1 @@ -MD5 (EMBOSS-1.0.0.tar.gz) = 7b8e7bebdef3adfb6fe45a2d346318fb +MD5 (EMBOSS-1.1.0.tar.gz) = 9de4ee8a02d397d154cad177b560eaaa diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa new file mode 100644 index 000000000000..4289821e32b0 --- /dev/null +++ b/biology/emboss/files/patch-aa @@ -0,0 +1,24 @@ +Add ${PREFIX}/etc as an acceptable location for emboss.default. (This should +be incorporated into the next version 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"); + } + ++ /* look for $(PREFIX)_ROOT/../emboss.default */ ++ ++ if (!prefixRootFile) { ++ ajFmtPrintS (&namRootStr, "%s/etc/%s.default", prefixRoot, prefix); ++ prefixRootFile = fopen (ajStrStr(namRootStr), "r"); ++ } ++ + if (namFileOrig) + (void) ajStrAppC (&namFileOrig, ", "); + (void) ajStrApp (&namFileOrig, namRootStr); diff --git a/biology/emboss/pkg-message b/biology/emboss/pkg-message new file mode 100644 index 000000000000..f14bff524b5a --- /dev/null +++ b/biology/emboss/pkg-message @@ -0,0 +1,22 @@ +-------------------------------------------------------------------------- + +The EMBOSS suite has been successfully installed. + +In order to use the EMBOSS programs, you will need to set some environment +variables in your shell startup file. If EMBOSS was installed to the +default prefix, then: + +- set PLPLOT_LIB to: "/usr/local/share/EMBOSS" +- set EMBOSS_ACDROOT to: "/usr/local/share/EMBOSS/acd" + +NB: A sample configuration file has been installed to /usr/local/etc as +emboss.default.sample. This must be renamed to emboss.default and edited +to suit your site and its requirements. + +A .embossrc in a user's home directory overrides settings in the +system-wide emboss.default. + +Further EMBOSS documentation is available at: + http://www.uk.embnet.org/Software/EMBOSS/Doc/ + +-------------------------------------------------------------------------- diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index 0f02fc997526..dd8d44bd0230 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -15,6 +15,7 @@ bin/cusp bin/cutseq bin/dan bin/dbiblast +bin/dbifasta bin/dbiflat bin/dbigcg bin/descseq @@ -102,6 +103,7 @@ bin/supermatcher bin/syco bin/textsearch bin/tfextract +bin/tfm bin/tfscan bin/tmap bin/transeq @@ -111,6 +113,7 @@ bin/wobble bin/wordcount bin/wordmatch bin/wossname +etc/emboss.default.sample lib/libplplot.so.4 lib/libplplot.so lib/libplplot.a @@ -123,6 +126,248 @@ lib/libajaxg.a lib/libnucleus.so.1 lib/libnucleus.so lib/libnucleus.a +share/doc/EMBOSS/manuals/Makefile +share/doc/EMBOSS/manuals/Makefile.am +share/doc/EMBOSS/manuals/Makefile.in +share/doc/EMBOSS/manuals/Makefile.in.orig +share/doc/EMBOSS/programs/html/Makefile +share/doc/EMBOSS/programs/html/Makefile.am +share/doc/EMBOSS/programs/html/Makefile.in +share/doc/EMBOSS/programs/html/Makefile.in.orig +share/doc/EMBOSS/programs/html/antigenic.html +share/doc/EMBOSS/programs/html/backtranseq.html +share/doc/EMBOSS/programs/html/banana.html +share/doc/EMBOSS/programs/html/chaos.html +share/doc/EMBOSS/programs/html/checktrans.html +share/doc/EMBOSS/programs/html/chips.html +share/doc/EMBOSS/programs/html/cirdna.html +share/doc/EMBOSS/programs/html/codcmp.html +share/doc/EMBOSS/programs/html/complex.html +share/doc/EMBOSS/programs/html/compseq.html +share/doc/EMBOSS/programs/html/cpgplot.html +share/doc/EMBOSS/programs/html/cpgreport.html +share/doc/EMBOSS/programs/html/cusp.html +share/doc/EMBOSS/programs/html/cutseq.html +share/doc/EMBOSS/programs/html/dan.html +share/doc/EMBOSS/programs/html/dbiblast.html +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/digest.html +share/doc/EMBOSS/programs/html/dotmatcher.html +share/doc/EMBOSS/programs/html/dottup.html +share/doc/EMBOSS/programs/html/dreg.html +share/doc/EMBOSS/programs/html/einverted.html +share/doc/EMBOSS/programs/html/embossdata.html +share/doc/EMBOSS/programs/html/emma.html +share/doc/EMBOSS/programs/html/equicktandem.html +share/doc/EMBOSS/programs/html/est2genome.html +share/doc/EMBOSS/programs/html/etandem.html +share/doc/EMBOSS/programs/html/extractseq.html +share/doc/EMBOSS/programs/html/findkm.html +share/doc/EMBOSS/programs/html/freak.html +share/doc/EMBOSS/programs/html/fuzznuc.html +share/doc/EMBOSS/programs/html/fuzzpro.html +share/doc/EMBOSS/programs/html/fuzztran.html +share/doc/EMBOSS/programs/html/garnier.html +share/doc/EMBOSS/programs/html/geecee.html +share/doc/EMBOSS/programs/html/getorf.html +share/doc/EMBOSS/programs/html/helixturnhelix.html +share/doc/EMBOSS/programs/html/iep.html +share/doc/EMBOSS/programs/html/infoseq.html +share/doc/EMBOSS/programs/html/isochore.html +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/merger.html +share/doc/EMBOSS/programs/html/msbar.html +share/doc/EMBOSS/programs/html/needle.html +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/nthseq.html +share/doc/EMBOSS/programs/html/octanol.html +share/doc/EMBOSS/programs/html/oddcomp.html +share/doc/EMBOSS/programs/html/palindrome.html +share/doc/EMBOSS/programs/html/pasteseq.html +share/doc/EMBOSS/programs/html/patmatdb.html +share/doc/EMBOSS/programs/html/patmatmotifs.html +share/doc/EMBOSS/programs/html/pepcoil.html +share/doc/EMBOSS/programs/html/pepinfo.html +share/doc/EMBOSS/programs/html/pepnet.html +share/doc/EMBOSS/programs/html/pepstats.html +share/doc/EMBOSS/programs/html/pepwheel.html +share/doc/EMBOSS/programs/html/pepwindow.html +share/doc/EMBOSS/programs/html/pepwindowall.html +share/doc/EMBOSS/programs/html/plotorf.html +share/doc/EMBOSS/programs/html/polydot.html +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/printsextract.html +share/doc/EMBOSS/programs/html/profit.html +share/doc/EMBOSS/programs/html/prophecy.html +share/doc/EMBOSS/programs/html/prophet.html +share/doc/EMBOSS/programs/html/prosextract.html +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/seealso.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/seqretset.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/splitter.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/syco.html +share/doc/EMBOSS/programs/html/textsearch.html +share/doc/EMBOSS/programs/html/tfextract.html +share/doc/EMBOSS/programs/html/tfm.html +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/water.html +share/doc/EMBOSS/programs/html/wobble.html +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/Makefile +share/doc/EMBOSS/programs/text/Makefile.am +share/doc/EMBOSS/programs/text/Makefile.in +share/doc/EMBOSS/programs/text/Makefile.in.orig +share/doc/EMBOSS/programs/text/antigenic.txt +share/doc/EMBOSS/programs/text/backtranseq.txt +share/doc/EMBOSS/programs/text/banana.txt +share/doc/EMBOSS/programs/text/chaos.txt +share/doc/EMBOSS/programs/text/checktrans.txt +share/doc/EMBOSS/programs/text/chips.txt +share/doc/EMBOSS/programs/text/cirdna.txt +share/doc/EMBOSS/programs/text/codcmp.txt +share/doc/EMBOSS/programs/text/complex.txt +share/doc/EMBOSS/programs/text/compseq.txt +share/doc/EMBOSS/programs/text/cpgplot.txt +share/doc/EMBOSS/programs/text/cpgreport.txt +share/doc/EMBOSS/programs/text/cusp.txt +share/doc/EMBOSS/programs/text/cutseq.txt +share/doc/EMBOSS/programs/text/dan.txt +share/doc/EMBOSS/programs/text/dbiblast.txt +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/digest.txt +share/doc/EMBOSS/programs/text/dotmatcher.txt +share/doc/EMBOSS/programs/text/dottup.txt +share/doc/EMBOSS/programs/text/dreg.txt +share/doc/EMBOSS/programs/text/einverted.txt +share/doc/EMBOSS/programs/text/embossdata.txt +share/doc/EMBOSS/programs/text/emma.txt +share/doc/EMBOSS/programs/text/equicktandem.txt +share/doc/EMBOSS/programs/text/est2genome.txt +share/doc/EMBOSS/programs/text/etandem.txt +share/doc/EMBOSS/programs/text/extractseq.txt +share/doc/EMBOSS/programs/text/findkm.txt +share/doc/EMBOSS/programs/text/freak.txt +share/doc/EMBOSS/programs/text/fuzznuc.txt +share/doc/EMBOSS/programs/text/fuzzpro.txt +share/doc/EMBOSS/programs/text/fuzztran.txt +share/doc/EMBOSS/programs/text/garnier.txt +share/doc/EMBOSS/programs/text/geecee.txt +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/merger.txt +share/doc/EMBOSS/programs/text/msbar.txt +share/doc/EMBOSS/programs/text/needle.txt +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/nthseq.txt +share/doc/EMBOSS/programs/text/octanol.txt +share/doc/EMBOSS/programs/text/oddcomp.txt +share/doc/EMBOSS/programs/text/palindrome.txt +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/pepcoil.txt +share/doc/EMBOSS/programs/text/pepinfo.txt +share/doc/EMBOSS/programs/text/pepnet.txt +share/doc/EMBOSS/programs/text/pepstats.txt +share/doc/EMBOSS/programs/text/pepwheel.txt +share/doc/EMBOSS/programs/text/pepwindow.txt +share/doc/EMBOSS/programs/text/pepwindowall.txt +share/doc/EMBOSS/programs/text/plotorf.txt +share/doc/EMBOSS/programs/text/polydot.txt +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/printsextract.txt +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/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/restrict.txt +share/doc/EMBOSS/programs/text/revseq.txt +share/doc/EMBOSS/programs/text/seealso.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/seqretset.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/splitter.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/syco.txt +share/doc/EMBOSS/programs/text/textsearch.txt +share/doc/EMBOSS/programs/text/tfextract.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/water.txt +share/doc/EMBOSS/programs/text/wobble.txt +share/doc/EMBOSS/programs/text/wordcount.txt +share/doc/EMBOSS/programs/text/wordmatch.txt +share/doc/EMBOSS/programs/text/wossname.txt +share/doc/EMBOSS/tutorials/Makefile +share/doc/EMBOSS/tutorials/Makefile.am +share/doc/EMBOSS/tutorials/Makefile.in +share/doc/EMBOSS/tutorials/Makefile.in.orig share/EMBOSS/plstnd5.fnt share/EMBOSS/plxtnd5.fnt share/EMBOSS/acd/ajbad.acd @@ -163,12 +408,13 @@ share/EMBOSS/acd/cusp.acd share/EMBOSS/acd/cutseq.acd share/EMBOSS/acd/dan.acd share/EMBOSS/acd/dbiblast.acd +share/EMBOSS/acd/dbifasta.acd share/EMBOSS/acd/dbiflat.acd share/EMBOSS/acd/dbigcg.acd share/EMBOSS/acd/descseq.acd share/EMBOSS/acd/digest.acd -share/EMBOSS/acd/dotmatcher.acd share/EMBOSS/acd/dottup.acd +share/EMBOSS/acd/dotmatcher.acd share/EMBOSS/acd/dreg.acd share/EMBOSS/acd/einverted.acd share/EMBOSS/acd/embossdata.acd @@ -213,8 +459,8 @@ share/EMBOSS/acd/pepnet.acd share/EMBOSS/acd/pepstats.acd share/EMBOSS/acd/pepwheel.acd share/EMBOSS/acd/pepwindow.acd -share/EMBOSS/acd/pepwindowall.acd share/EMBOSS/acd/plotorf.acd +share/EMBOSS/acd/pepwindowall.acd share/EMBOSS/acd/polydot.acd share/EMBOSS/acd/preg.acd share/EMBOSS/acd/prettyplot.acd @@ -236,8 +482,8 @@ share/EMBOSS/acd/seqret.acd share/EMBOSS/acd/seqretall.acd share/EMBOSS/acd/seqretset.acd share/EMBOSS/acd/seqretsplit.acd -share/EMBOSS/acd/showdb.acd share/EMBOSS/acd/seqrettype.acd +share/EMBOSS/acd/showdb.acd share/EMBOSS/acd/showfeat.acd share/EMBOSS/acd/showorf.acd share/EMBOSS/acd/showseq.acd @@ -250,6 +496,7 @@ share/EMBOSS/acd/supermatcher.acd share/EMBOSS/acd/syco.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 @@ -640,12 +887,18 @@ share/EMBOSS/test/wormpep/acnum.trg share/EMBOSS/test/wormpep/division.lkp share/EMBOSS/test/wormpep/entrynam.idx share/EMBOSS/test/wormpep/wormpep +@dirrm share/doc/EMBOSS/manuals +@dirrm share/doc/EMBOSS/programs/html +@dirrm share/doc/EMBOSS/programs/text +@dirrm share/doc/EMBOSS/programs +@dirrm share/doc/EMBOSS/tutorials +@dirrm share/doc/EMBOSS +@dirrm share/EMBOSS/acd @dirrm share/EMBOSS/data/CODONS @dirrm share/EMBOSS/data/REBASE @dirrm share/EMBOSS/data/PRINTS @dirrm share/EMBOSS/data/PROSITE @dirrm share/EMBOSS/data -@dirrm share/EMBOSS/acd @dirrm share/EMBOSS/test/data @dirrm share/EMBOSS/test/embl @dirrm share/EMBOSS/test/pir |