diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/Makefile | 46 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/distinfo | 1 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/Makefile | 8 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/freebsd.ncbi.mk | 27 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-aa | 177 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-ab | 19 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-ac | 11 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-descr | 16 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-plist | 69 |
11 files changed, 376 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index b41533083b49..bc2c4d1d767f 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -14,6 +14,7 @@ SUBDIR += molden SUBDIR += mopac SUBDIR += nab + SUBDIR += ncbi-toolkit SUBDIR += ortep3 SUBDIR += p5-AcePerl SUBDIR += p5-bioperl diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile new file mode 100644 index 000000000000..cd425388a9b9 --- /dev/null +++ b/biology/ncbi-toolkit/Makefile @@ -0,0 +1,46 @@ +# New ports collection makefile for: NCBI +# Date created: 03 April 2000 +# Whom: tonym +# +# $FreeBSD$ +# + +PORTNAME= ncbi.toolkit +PORTVERSION= 2000.07.07 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/ +DISTNAME= ncbi +DIST_SUBDIR= ncbi + +MAINTAINER= tony.maher@ebioinformatics.com + +REQUIRES_MOTIF= yes + +# +# In the files directory we have: +# + +DUMMYMAKE= Makefile + +# +# out of it for the post-install when we put in system startup file. +# + +PLATFORMDIR= ${WRKSRC}/platform +BUILDSCRIPT= ${WRKSRC}/make/makedis.csh + +# +# Thus ends the definitions +# + +# +# We need a dummy top level Makefile as NCBI has scripts that need to +# run from point above ncbi hierachy. +# + +pre-configure: + @${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC} + @${CP} ${FILESDIR}/freebsd.ncbi.mk ${PLATFORMDIR} + @${PERL} -pi.orig -e 's#NetBSD#FreeBSD#;' -e 's#netbsd#freebsd#' ${BUILDSCRIPT} + +.include <bsd.port.mk> diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo new file mode 100644 index 000000000000..51b43743b473 --- /dev/null +++ b/biology/ncbi-toolkit/distinfo @@ -0,0 +1 @@ +MD5 (ncbi/ncbi.tar.gz) = d201fc46e5e31e930ab73cc2dab79a2e diff --git a/biology/ncbi-toolkit/files/Makefile b/biology/ncbi-toolkit/files/Makefile new file mode 100644 index 000000000000..ee0f54493ca9 --- /dev/null +++ b/biology/ncbi-toolkit/files/Makefile @@ -0,0 +1,8 @@ +# +# $FreeBSD$ + +all: + cd ..; ./ncbi/make/makedis.csh + +install: + cd build; $(MAKE) install diff --git a/biology/ncbi-toolkit/files/freebsd.ncbi.mk b/biology/ncbi-toolkit/files/freebsd.ncbi.mk new file mode 100644 index 000000000000..91abd596fbbc --- /dev/null +++ b/biology/ncbi-toolkit/files/freebsd.ncbi.mk @@ -0,0 +1,27 @@ +# +# $Id$ freebsd.ncbi.mk +# +# That platform is not supported and is contributed to NCBI by +# freebsd-bio@freebsd.net +# +NCBI_DEFAULT_LCL = bsd +NCBI_MAKE_SHELL = /bin/sh +NCBI_CC = cc +NCBI_CFLAGS1 = ${CFLAGS} -c +NCBI_LDFLAGS1 = -O +NCBI_OPTFLAG = +NCBI_BIN_MASTER = /home/coremake/ncbi/bin +NCBI_BIN_COPY = /home/coremake/ncbi/bin +NCBI_INCDIR = /home/coremake/ncbi/include +NCBI_LIBDIR = /home/coremake/ncbi/lib +NCBI_ALTLIB = /home/coremake/ncbi/altlib +#will work only when you have Motif installed! +NCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF +NCBI_VIBLIBS = -lXm -lXmu -lXp -lXpm -lXt -lX11 -lXext +NCBI_DISTVIBLIBS = -L/usr/X11R6/lib /usr/X11R6/lib/libXm.a /usr/X11R6/lib/libXp.a /usr/X11R6/lib/libXpm.a -lXmu -lXt -lX11 -lXext +NCBI_OTHERLIBS = -lm +NCBI_RANLIB = ranlib +# Used by makedis.csh +NCBI_MT_OTHERLIBS = +NCBI_THREAD_OBJ = ncbithr.o +NETENTREZVERSION = 2.02c2ASN1SPEC6 diff --git a/biology/ncbi-toolkit/files/patch-aa b/biology/ncbi-toolkit/files/patch-aa new file mode 100644 index 000000000000..bffe73899634 --- /dev/null +++ b/biology/ncbi-toolkit/files/patch-aa @@ -0,0 +1,177 @@ +--- make/makeall.unx.orig Sat Jul 8 04:16:35 2000 ++++ make/makeall.unx Tue Oct 24 22:35:34 2000 +@@ -782,3 +782,174 @@ + #load $(LDFLAGS) getmuid.c medutil.c \ + $(SRC11) $(SRC8) $(SRC7) $(SRC6) $(SRC5) $(SRC3) \ + $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl ++ ++EXE= Cn3Dv3d Nentrez Psequin \ ++ asn2fast asn2ff asndhuff asntool \ ++ bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \ ++ cdscan checksub copymat \ ++ ddv dosimple \ ++ entrcmd errhdr fa2htgs fastacmd findspl fmerge formatdb \ ++ getfeat getmesh getpub getseq gil2bin \ ++ idfetch impala indexpub \ ++ makemat makeset megablast \ ++ ncbisort netentcf \ ++ rpsblast \ ++ seedtop seqtest \ ++ tbl2asn testcore testobj testval \ ++ udv vecscreen ++ ++ ++LIB= libncbi.a libncbicdr.a libncbimla.a libncbitxc2.a \ ++ libnetentr.a libncbiCacc.a libncbicn3d.a libncbimmdb.a \ ++ libnetblast.a libvibgif.a libncbiNacc.a libncbidesk.a \ ++ libncbiobj.a libnetcli.a libvibnet.a libncbiacc.a \ ++ libncbiid1.a libncbitool.a libnetcli_.a libvibrant.a ++ ++ ++INC= actutils.h matrix.h rpsutil.h \ ++ asnblock.h mbalign.h saldist.h \ ++ asncode.h mblast.h saled.h \ ++ asnent2.h mbutils.h saledit.h \ ++ asnfdef.h mconsist.h salfiles.h \ ++ asnfeat.h mdrcherr.h salign.h \ ++ asngen.h medarch.h salmedia.h \ ++ asnid0.h medutil.h salogif.h \ ++ asnloc.h medview.h salpacc.h \ ++ asnmdrs.h mkbioseq.h salpanel.h \ ++ asnmedli.h mmdb1.h salparam.h \ ++ asnmime.h mmdb2.h salpedit.h \ ++ asnmla.h mmdb3.h salprop.h \ ++ asnneten.h mmdbapi.h salpstat.h \ ++ asnproj.h mmdbapi1.h salptool.h \ ++ asnprt.h mmdbapi2.h salsa.h \ ++ asnpub.h mmdbapi3.h salsap.h \ ++ asnpubme.h mmdbapi4.h salstruc.h \ ++ asnres.h mmdbdata.h salutil.h \ ++ asnseq.h mmdblocl.h samutil.h \ ++ asnsset.h ncbi.h satutil.h \ ++ asnsubmt.h ncbibs.h sdisplay.h \ ++ asntax1.h ncbibuf.h sec.h \ ++ asntaxon.h ncbicli.h seed.h \ ++ bandalgn.h ncbidraw.h seg.h \ ++ binary.h ncbienv.h seqanal.h \ ++ biosrc.h ncbierr.h seqcons.h \ ++ blast.h ncbifile.h seqfltr.h \ ++ blastdef.h ncbigif.h seqgraph.h \ ++ blastkar.h ncbilang.h seqgrphx.h \ ++ blastpat.h ncbilcl.h seqmgr.h \ ++ blastpri.h ncbimain.h seqmtrx.h \ ++ blocks.h ncbimath.h seqpcc.h \ ++ blstspc.h ncbimem.h seqport.h \ ++ bspview.h ncbimisc.h seqscrl.h \ ++ casn.h ncbimsg.h seqsub.h \ ++ cdconfig.h ncbinet.h sequtil.h \ ++ cdd.h ncbiopt.h shim3d.h \ ++ cdentrez.h ncbiport.h simple.h \ ++ cdnewlib.h ncbiprop.h simutil.h \ ++ cdrgn.h ncbisam.h spell.h \ ++ cdrom.h ncbisami.h splutil.h \ ++ cdromlib.h ncbisgml.h sqnutils.h \ ++ cn3dentr.h ncbisock.h strimprt.h \ ++ cn3dmain.h ncbisort.h stsutil.h \ ++ cn3dmesh.h ncbisrti.h subutil.h \ ++ cn3dmodl.h ncbistd.h suggapi.h \ ++ cn3dmsel.h ncbistr.h suggen.h \ ++ cn3dmsg.h ncbithr.h suggest.h \ ++ cn3dopen.h ncbitime.h suggslp.h \ ++ cn3dsave.h ncbiurl.h sugmap.h \ ++ cn3dshim.h ncbiwin.h sugprefx.h \ ++ cn3dstyl.h ncbiwww.h tax0.h \ ++ cn3dxprt.h netblap3.h tax1map.h \ ++ codon.h netcnfg.h taxblast.h \ ++ con_file.h netentr.h taxext.h \ ++ con_sock.h netlib.h taxinc.h \ ++ con_stateless.h netpriv.h taxon1.h \ ++ con_url.h netscape.h taxuerr.h \ ++ ni_asn.h taxutil.h \ ++ connectn.h ni_defin.h terr.h \ ++ connectr.h ni_encr.h tfuns.h \ ++ connutil.h ni_error.h toasn3.h \ ++ corematx.h ni_lib.h tofasta.h \ ++ db_list.h ni_lib_.h tofile.h \ ++ ddvclick.h ni_list.h tomedlin.h \ ++ ddvcolor.h ni_msg.h toporg.h \ ++ ddvcreate.h ni_net.h tree.h \ ++ ddvgraph.h ni_types.h treemgr.h \ ++ ddvmain.h objacces.h treeview.h \ ++ ddvopen.h objalign.h treevint.h \ ++ ddvpanel.h objalignloc.h tsprintf.h \ ++ diagnost.h objall.h txalign.h \ ++ dlogutil.h objbibli.h txclient.h \ ++ document.h objblock.h txcommon.h \ ++ dotmatrx.h objblst3.h udvdef.h \ ++ drawingp.h objcdd.h udviewer.h \ ++ drawseq.h objcode.h udvseq.h \ ++ dust.h objent2.h undefwin.h \ ++ dvncode.h objentr.h urkbias.h \ ++ echo_asn.h objfdef.h urkcnsrt.h \ ++ edutil.h objfeat.h urkdust.h \ ++ ent2api.h objgen.h urkepi.h \ ++ entrez.h objloc.h urkfltr.h \ ++ errdefn.h objmdrs.h urkgraph.h \ ++ explore.h objmedli.h urkpcc.h \ ++ fea2seg.h objmgr.h urkptpf.h \ ++ ffprint.h objmime.h urksigu.h \ ++ findrepl.h objmla.h urktree.h \ ++ fstyle.h objmmdb1.h urkutil.h \ ++ fstylep.h objmmdb2.h urlquery.h \ ++ ftusrstr.h objmmdb3.h utilpars.h \ ++ gapxdrop.h objneten.h utilpub.h \ ++ gather.h objproj.h valid.h \ ++ gbfeat.h objprt.h validatr.h \ ++ gbftdef.h objpub.h validerr.h \ ++ gbparlex.h objpubd.h vast2cn3d.h \ ++ gifgen.h objpubme.h vast2mage.h \ ++ glbpic.h objres.h vast2pdb.h \ ++ gphdraw.h objseq.h vastlocl.h \ ++ gtrdraw.h objsset.h vastsrv.h \ ++ gxydraw.h objsub.h vecscnapi.h \ ++ id1.h objtax1.h vecscrn.h \ ++ id1arch.h objtaxc0.h vibdefns.h \ ++ id1gen.h odlbox.h vibfltr.h \ ++ id1map.h panels.h vibforms.h \ ++ image.h parsegb.h vibgraph.h \ ++ imagelst.h pdiagnos.h vibincld.h \ ++ import.h pgppop.h vibmouse.h \ ++ jzcoll.h pictur3d.h vibpcc.h \ ++ jzmisc.h picture.h vibprocs.h \ ++ layout.h picturep.h vibrant.h \ ++ lbapi.h pmfapi.h vibtree.h \ ++ legend.h pobutil.h vibtypes.h \ ++ list.h posit.h viewer.h \ ++ lnfac.h ppict3d.h viewer3d.h \ ++ lookup.h profiles.h viewerp.h \ ++ lsqfetch.h prtgene.h viewmgr.h \ ++ mapgene.h prtutil.h vsm.h \ ++ mapmime.h prunebsc.h vsmfile.h \ ++ mapmla.h pubdesc.h vsmpriv.h \ ++ mappingp.h puberr.h vsmutil.h \ ++ mapproj.h qblastapi.h wwwblast.h \ ++ mappubme.h readdb.h \ ++ maputil.h regex.h ++ ++MKDIR= /bin/mkdir -p ++INSTALL_PROGRAM= /usr/bin/install -c ++ ++binstall: $(EXE) ++ ${MKDIR} ${PREFIX}/bin ++ ${INSTALL_PROGRAM} -s $? /${PREFIX}/bin ++ ++linstall: $(LIB) ++ ${MKDIR} ${PREFIX}/lib/ncbi ++ ${INSTALL_PROGRAM} $? ${PREFIX}/lib/ncbi ++ ++iinstall:: ++ ${MKDIR} ${PREFIX}/include/ncbi ++ pwd ++ cd ../include; \ ++ for file in $(INC); do \ ++ ${INSTALL_PROGRAM} $$file ${PREFIX}/include/ncbi; \ ++ done ++ ++install: linstall binstall ++ diff --git a/biology/ncbi-toolkit/files/patch-ab b/biology/ncbi-toolkit/files/patch-ab new file mode 100644 index 000000000000..886047ae18c8 --- /dev/null +++ b/biology/ncbi-toolkit/files/patch-ab @@ -0,0 +1,19 @@ +--- corelib/ncbilcl.bsd.orig Mon Apr 3 08:50:57 2000 ++++ corelib/ncbilcl.bsd Mon Apr 3 08:51:55 2000 +@@ -74,7 +74,6 @@ + #include <stdio.h> + #include <ctype.h> + #include <string.h> +-#include <malloc.h> + #include <memory.h> + #include <stdlib.h> + #include <math.h> +@@ -84,7 +83,7 @@ + + /* Check if there are POSIX threads available */ + #ifdef _POSIX_THREADS +-#define POSIX_THREADS_AVAIL ++#define POSIX_THREADS_AVAIL_broken + #endif + + diff --git a/biology/ncbi-toolkit/files/patch-ac b/biology/ncbi-toolkit/files/patch-ac new file mode 100644 index 000000000000..3099d88124c9 --- /dev/null +++ b/biology/ncbi-toolkit/files/patch-ac @@ -0,0 +1,11 @@ +--- corelib/ncbienv.c.orig Tue Jan 25 08:16:49 2000 ++++ corelib/ncbienv.c Mon Apr 3 08:56:02 2000 +@@ -183,6 +183,8 @@ + + #ifdef OS_UNIX + #include <pwd.h> ++#include <sys/param.h> ++#define LOGNAME_MAX MAXLOGNAME + #endif /* OS_UNIX */ + #ifdef OS_MAC + #include <Gestalt.h> diff --git a/biology/ncbi-toolkit/pkg-comment b/biology/ncbi-toolkit/pkg-comment new file mode 100644 index 000000000000..29c8ef1ede95 --- /dev/null +++ b/biology/ncbi-toolkit/pkg-comment @@ -0,0 +1 @@ +National Center for Biotechnology Information (NCBI) Development Toolkit. diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr new file mode 100644 index 000000000000..5a683434f4cb --- /dev/null +++ b/biology/ncbi-toolkit/pkg-descr @@ -0,0 +1,16 @@ +"The NCBI Software Development Toolkit was developed for the production and +distribution of GenBank, Entrez, BLAST, and related services by NCBI. We +make it freely available to the public without restriction to facilitate the +use of NCBI by the scientific community. However, please understand that +while we feel we have done a high quality job, this is not commercial +software. +The documentation lags considerably behind the software and we must make any +changes required by our data production needs. Nontheless, many people have +found it a useful and stable basis for a number of tools and applications. + +The toolkit is available by anonymous ftp from ncbi.nlm.nih.gov" + +excerpt from NCBI toolkit README file. + +-- Tony Maher <tony.maher@ebioinformatics.com> + FreeBSD bio-porters <bio@freebsd.net> diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist new file mode 100644 index 000000000000..6b84087bd47f --- /dev/null +++ b/biology/ncbi-toolkit/pkg-plist @@ -0,0 +1,69 @@ +bin/Cn3Dv3d +bin/Nentrez +bin/Psequin +bin/asn2fast +bin/asn2ff +bin/asndhuff +bin/asntool +bin/bl2seq +bin/blast.REAL +bin/blastall +bin/blastcl3 +bin/blastclust +bin/blastpgp +bin/cdscan +bin/checksub +bin/copymat +bin/ddv +bin/dosimple +bin/entrcmd +bin/errhdr +bin/fa2htgs +bin/fastacmd +bin/findspl +bin/fmerge +bin/formatdb +bin/getfeat +bin/getmesh +bin/getpub +bin/getseq +bin/gil2bin +bin/idfetch +bin/impala +bin/indexpub +bin/makemat +bin/makeset +bin/megablast +bin/ncbisort +bin/netentcf +bin/rpsblast +bin/seedtop +bin/seqtest +bin/tbl2asn +bin/testcore +bin/testobj +bin/testval +bin/udv +bin/vecscreen +lib/ncbi/libncbi.a +lib/ncbi/libncbicdr.a +lib/ncbi/libncbimla.a +lib/ncbi/libncbitxc2.a +lib/ncbi/libnetentr.a +lib/ncbi/libncbiCacc.a +lib/ncbi/libncbicn3d.a +lib/ncbi/libncbimmdb.a +lib/ncbi/libnetblast.a +lib/ncbi/libvibgif.a +lib/ncbi/libncbiNacc.a +lib/ncbi/libncbidesk.a +lib/ncbi/libncbiobj.a +lib/ncbi/libnetcli.a +lib/ncbi/libvibnet.a +lib/ncbi/libncbiacc.a +lib/ncbi/libncbiid1.a +lib/ncbi/libncbitool.a +lib/ncbi/libnetcli_.a +lib/ncbi/libvibrant.a +@unexec rmdir %D/lib/ncbi +@unexec rm -rf %D/include/ncbi |