freebsd-ports/biology/emboss/pkg-plist
Thierry Thomas 10570c91c8 For EMBOSS:
This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 09:43:21 +00:00

2071 lines
81 KiB
Text

bin/aaindexextract
bin/abiview
bin/acdc
bin/acdpretty
bin/acdtable
bin/acdtrace
bin/acdvalid
bin/antigenic
bin/backtranseq
bin/banana
bin/biosed
bin/btwisted
bin/cai
bin/chaos
bin/charge
bin/checktrans
bin/chips
bin/cirdna
bin/codcmp
bin/codcopy
bin/coderet
bin/compseq
bin/cons
bin/cpgplot
bin/cpgreport
bin/cusp
bin/cutgextract
bin/dan
bin/cutseq
bin/dbiblast
bin/dbifasta
bin/dbiflat
bin/dbigcg
bin/dbxfasta
bin/dbxflat
bin/dbxgcg
bin/degapseq
bin/descseq
bin/diffseq
bin/digest
bin/distmat
bin/dotmatcher
bin/dotpath
bin/dottup
bin/dreg
bin/einverted
bin/embossdata
bin/embossversion
bin/emma
bin/emowse
bin/entret
bin/epestfind
bin/eprimer3
bin/equicktandem
bin/est2genome
bin/etandem
bin/extractfeat
bin/extractseq
bin/findkm
bin/freak
bin/fuzznuc
bin/fuzzpro
bin/fuzztran
bin/garnier
bin/geecee
bin/getorf
bin/helixturnhelix
bin/hmoment
bin/iep
bin/infoalign
bin/infoseq
bin/isochore
bin/jembossctl
bin/lindna
bin/listor
bin/marscan
bin/maskfeat
bin/maskseq
bin/matcher
bin/megamerger
bin/merger
bin/msbar
bin/mwcontam
bin/mwfilter
bin/needle
bin/newcpgreport
bin/newcpgseek
bin/newseq
bin/noreturn
bin/notseq
bin/nthseq
bin/octanol
bin/oddcomp
bin/palindrome
bin/pasteseq
bin/patmatdb
bin/patmatmotifs
bin/pepcoil
bin/pepinfo
bin/pepnet
bin/pepstats
bin/pepwheel
bin/pepwindow
bin/pepwindowall
bin/plotcon
bin/plotorf
bin/polydot
bin/preg
bin/prettyplot
bin/prettyseq
bin/primersearch
bin/printsextract
bin/profit
bin/prophecy
bin/prophet
bin/prosextract
bin/pscan
bin/psiphi
bin/rebaseextract
bin/recoder
bin/redata
bin/remap
bin/restover
bin/restrict
bin/revseq
bin/seealso
bin/seqmatchall
bin/seqret
bin/seqretsplit
bin/showalign
bin/showdb
bin/showfeat
bin/showorf
bin/showseq
bin/shuffleseq
bin/sigcleave
bin/silent
bin/sirna
bin/sixpack
bin/skipseq
bin/syco
bin/splitter
bin/stretcher
bin/stssearch
bin/supermatcher
bin/tcode
bin/textsearch
bin/tfextract
bin/tfm
bin/tfscan
bin/tmap
bin/tranalign
bin/transeq
bin/trimest
bin/trimseq
bin/twofeat
bin/union
bin/vectorstrip
bin/water
bin/whichdb
bin/wobble
bin/wordcount
bin/wordmatch
bin/wossname
bin/yank
bin/runJemboss.csh
include/drivers.h
include/pdf.h
include/plcore.h
include/plevent.h
include/plplotP.h
include/plxwd.h
include/metadefs.h
include/plConfig.h
include/pldebug.h
include/plplot.h
include/plstrm.h
include/plDevs.h
include/ajax.h
include/ajarch.h
include/ajdefine.h
include/ajacd.h
include/ajalign.h
include/ajarr.h
include/ajassert.h
include/ajbase.h
include/ajcall.h
include/ajcod.h
include/ajdan.h
include/ajdmx.h
include/ajdomain.h
include/ajexcept.h
include/ajfeat.h
include/ajfeatdata.h
include/ajfile.h
include/ajfmt.h
include/ajgraph.h
include/ajgraphxml.h
include/ajgraphstruct.h
include/ajhist.h
include/ajindex.h
include/ajjava.h
include/ajlist.h
include/ajmath.h
include/ajmatrices.h
include/ajmem.h
include/ajmess.h
include/ajnam.h
include/ajnexus.h
include/ajpdb.h
include/ajpdbio.h
include/ajphylo.h
include/ajrange.h
include/ajreg.h
include/ajreport.h
include/ajseq.h
include/ajseqabi.h
include/ajseqdata.h
include/ajseqdb.h
include/ajseqread.h
include/ajseqtype.h
include/ajseqwrite.h
include/ajsort.h
include/ajstr.h
include/ajsys.h
include/ajtable.h
include/ajtime.h
include/ajtranslate.h
include/ajtree.h
include/ajutil.h
include/ajvector.h
include/pcre.h
include/pcre_chartables.c
include/pcre_config.h
include/pcre_get.c
include/pcre_printint.c
include/pcre_internal.h
include/pcreposix.h
include/emboss.h
include/embaln.h
include/embcom.h
include/embcons.h
include/embdata.h
include/embdbi.h
include/embdmx.h
include/embdomain.h
include/embest.h
include/embexit.h
include/embgroup.h
include/embiep.h
include/embindex.h
include/embinit.h
include/embmat.h
include/embmisc.h
include/embmol.h
include/embnmer.h
include/embpat.h
include/embprop.h
include/embpdb.h
include/embread.h
include/embsig.h
include/embshow.h
include/embword.h
lib/libplplot.so.5
lib/libplplot.so
lib/libplplot.la
lib/libplplot.a
lib/libajax.so.3
lib/libajax.so
lib/libajax.la
lib/libajax.a
lib/libajaxg.so.3
lib/libajaxg.so
lib/libajaxg.la
lib/libajaxg.a
lib/libnucleus.so.3
lib/libnucleus.so
lib/libnucleus.la
lib/libnucleus.a
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@dirrm %%DATADIR%%/data/AAINDEX
@dirrm %%DATADIR%%/data/CODONS
@dirrm %%DATADIR%%/data/REBASE
@dirrm %%DATADIR%%/data/PRINTS
@dirrm %%DATADIR%%/data/PROSITE
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@dirrm %%DATADIR%%/test/embl
@dirrm %%DATADIR%%/test/genbank
@dirrm %%DATADIR%%/test/gb
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@dirrm %%DATADIR%%/jemboss/lib
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@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
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@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
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@dirrm %%DATADIR%%/jemboss/org
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@dirrm %%DATADIR%%/jemboss/utils
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@dirrmtry %%DATADIR%%
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