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Update to emboss 1.4.0.

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PR:		ports/20898
Submitted by:	Johann Visagie <johann@egenetics.com>
This commit is contained in:
Neil Blakey-Milner 2000-09-07 14:02:52 +00:00
parent 3d01e462f6
commit f4b4dfe07c
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=32388
4 changed files with 83 additions and 52 deletions
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20
biology/emboss/Makefile
View File

@ -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>

2
biology/emboss/distinfo
View File

@ -1 +1 @@
MD5 (EMBOSS-1.1.0.tar.gz) = 9de4ee8a02d397d154cad177b560eaaa
MD5 (EMBOSS-1.4.0.tar.gz) = ba096906cc10d0badbc1c479e61926c9

32
biology/emboss/files/patch-aa
View File

@ -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);

81
biology/emboss/pkg-plist
View File

@ -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