diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile new file mode 100644 index 00000000000..28c7a21bb6c --- /dev/null +++ b/biology/emboss/Makefile @@ -0,0 +1,44 @@ +# $OpenBSD: Makefile,v 1.1.1.1 2007/09/25 08:23:02 steven Exp $ + +COMMENT= European Molecular Biology Open Software Suite + +DISTNAME= EMBOSS-5.0.0 +PKGNAME= ${DISTNAME:L} +SHARED_LIBS += eplplot 0.0 # .5.7 +SHARED_LIBS += ajax 0.0 # .5.0 +SHARED_LIBS += ajaxg 0.0 # .5.0 +SHARED_LIBS += nucleus 0.0 # .5.0 + +CATEGORIES= biology + +HOMEPAGE= http://emboss.sourceforge.net/ + +# GPL v2 +PERMIT_PACKAGE_FTP= Yes +PERMIT_PACKAGE_CDROM= Yes +PERMIT_DISTFILES_FTP= Yes +PERMIT_DISTFILES_CDROM= Yes + +MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ + +WANTLIB= X11 Xau Xdmcp c m + +USE_X11= Yes +USE_LIBTOOL= Yes +CONFIGURE_STYLE=gnu +CONFIGURE_ENV= CPPFLAGS="-I${LOCALBASE}/include" \ + LDFLAGS="-L${LOCALBASE}/lib" + +DOC_DIRS= manuals tutorials programs/text programs/html + +pre-configure: +.for d in ${DOC_DIRS} + perl -pi -e \ + 's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$(datadir)/doc/\$$(PACKAGE)#' \ + ${WRKSRC}/doc/$d/Makefile.in +.endfor + +post-install: + rm -f ${PREFIX}/include/pcre* + +.include diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo new file mode 100644 index 00000000000..fa98d065c48 --- /dev/null +++ b/biology/emboss/distinfo @@ -0,0 +1,5 @@ +MD5 (EMBOSS-5.0.0.tar.gz) = vkyJUiCtNK/WXUULp9jjSw== +RMD160 (EMBOSS-5.0.0.tar.gz) = G/UQwJGdmR5LpnGCE3RI3uSbq00= +SHA1 (EMBOSS-5.0.0.tar.gz) = GtTtxICKgiX+jVdOin0Ghr6ZysY= +SHA256 (EMBOSS-5.0.0.tar.gz) = ZObwm4KnGf8m3n8h/ffSvWBdLGZDhMHHtI+dJF1fQK4= +SIZE (EMBOSS-5.0.0.tar.gz) = 20666560 diff --git a/biology/emboss/pkg/DESCR b/biology/emboss/pkg/DESCR new file mode 100644 index 00000000000..eaa636a5b90 --- /dev/null +++ b/biology/emboss/pkg/DESCR @@ -0,0 +1,10 @@ +EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS +is a free Open Source software analysis package specially developed for +the needs of the molecular biology (e.g. EMBnet) user community. The +software automatically copes with data in a variety of formats and even +allows transparent retrieval of sequence data from the web. Also, as +extensive libraries are provided with the package, it is a platform to +allow other scientists to develop and release software in true open +source spirit. EMBOSS also integrates a range of currently available +packages and tools for sequence analysis into a seamless whole. EMBOSS +breaks the historical trend towards commercial software packages. diff --git a/biology/emboss/pkg/PFRAG.shared b/biology/emboss/pkg/PFRAG.shared new file mode 100644 index 00000000000..40f80529ef5 --- /dev/null +++ b/biology/emboss/pkg/PFRAG.shared @@ -0,0 +1,5 @@ +@comment $OpenBSD: PFRAG.shared,v 1.1.1.1 2007/09/25 08:23:04 steven Exp $ +@lib lib/libajax.so.${LIBajax_VERSION} +@lib lib/libajaxg.so.${LIBajaxg_VERSION} +@lib lib/libeplplot.so.${LIBeplplot_VERSION} +@lib lib/libnucleus.so.${LIBnucleus_VERSION} diff --git a/biology/emboss/pkg/PLIST b/biology/emboss/pkg/PLIST new file mode 100644 index 00000000000..8849d90e2e7 --- /dev/null +++ b/biology/emboss/pkg/PLIST @@ -0,0 +1,1832 @@ +@comment $OpenBSD: PLIST,v 1.1.1.1 2007/09/25 08:23:04 steven Exp $ +%%SHARED%% +bin/aaindexextract +bin/abiview +bin/acdc +bin/acdpretty +bin/acdtable +bin/acdtrace +bin/acdvalid +bin/antigenic +bin/backtranambig +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/cutseq +bin/dan +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/edialign +bin/einverted +bin/embossdata +bin/embossversion +bin/emma +bin/emowse +bin/entret +bin/epestfind +bin/eprimer3 +bin/equicktandem +bin/est2genome +bin/etandem +bin/extractalign +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/makenucseq +bin/makeprotseq +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/runJemboss.csh +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/splitter +bin/stretcher +bin/stssearch +bin/supermatcher +bin/syco +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/wordfinder +bin/wordmatch +bin/wossname +bin/yank +include/ajacd.h +include/ajalign.h +include/ajarch.h +include/ajarr.h +include/ajassert.h +include/ajax.h +include/ajbase.h +include/ajcall.h +include/ajcod.h +include/ajdan.h +include/ajdefine.h +include/ajdmx.h +include/ajdom.h +include/ajdomain.h +include/ajexcept.h +include/ajfeat.h +include/ajfeatdata.h +include/ajfile.h +include/ajfmt.h +include/ajgraph.h +include/ajgraphstruct.h +include/ajgraphxml.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/ajpat.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 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