New Port: biology/ncbi-toolkit

National Center for Biotechnology Information (NCBI) Development Toolkit.

PR:		22388
Submitted by:	Tony Maher <tony.maher@ebioinformatics.com>

10 files changed, 375 insertions, 0 deletions

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