Date: Sun, 29 Oct 2000 19:10:14 +1100 (EST) From: tony.maher@ebioinformatics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/22388: New port: biology/ncbi.toolkit Message-ID: <200010290810.e9T8AEg01078@dt.home>
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>Number: 22388
>Category: ports
>Synopsis: New port: biology/ncbi.toolkit
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Sun Oct 29 01:20:01 PDT 2000
>Closed-Date:
>Last-Modified:
>Originator: Tony Maher
>Release: FreeBSD 4.1.1-STABLE i386
>Organization:
eBioinformatics
>Environment:
>Description:
This is port of the NCBI toolkit that is available by anonymous ftp from
ncbi.nlm.nih.gov
I have not gotten explicit permission for the toolkit to be distributed
via cdrom but the README file states:
"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."
and the Copyright code on the source files carries similar message.
So I don't see any problem with its inclusion.
There are some improvements I'd like to see made to this port
but it _is_ fully functional and numerous people would actually like
to use it now!
>How-To-Repeat:
>Fix:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# ncbi.toolkit
# ncbi.toolkit/files
# ncbi.toolkit/files/Makefile
# ncbi.toolkit/files/freebsd.ncbi.mk
# ncbi.toolkit/files/patch-aa
# ncbi.toolkit/files/patch-ab
# ncbi.toolkit/files/patch-ac
# ncbi.toolkit/distinfo
# ncbi.toolkit/Makefile
# ncbi.toolkit/pkg-descr
# ncbi.toolkit/pkg-comment
# ncbi.toolkit/pkg-plist
#
echo c - ncbi.toolkit
mkdir -p ncbi.toolkit > /dev/null 2>&1
echo c - ncbi.toolkit/files
mkdir -p ncbi.toolkit/files > /dev/null 2>&1
echo x - ncbi.toolkit/files/Makefile
sed 's/^X//' >ncbi.toolkit/files/Makefile << 'END-of-ncbi.toolkit/files/Makefile'
X#
X#
X
Xall:
X cd ..; ./ncbi/make/makedis.csh
X
Xinstall:
X cd build; $(MAKE) install
END-of-ncbi.toolkit/files/Makefile
echo x - ncbi.toolkit/files/freebsd.ncbi.mk
sed 's/^X//' >ncbi.toolkit/files/freebsd.ncbi.mk << 'END-of-ncbi.toolkit/files/freebsd.ncbi.mk'
X#
X# $Id$ freebsd.ncbi.mk
X#
X# That platform is not supported and is contributed to NCBI by
X# freebsd-bio@freebsd.net
X#
XNCBI_DEFAULT_LCL = bsd
XNCBI_MAKE_SHELL = /bin/sh
XNCBI_CC = cc
XNCBI_CFLAGS1 = ${CFLAGS} -c
XNCBI_LDFLAGS1 = -O
XNCBI_OPTFLAG =
XNCBI_BIN_MASTER = /home/coremake/ncbi/bin
XNCBI_BIN_COPY = /home/coremake/ncbi/bin
XNCBI_INCDIR = /home/coremake/ncbi/include
XNCBI_LIBDIR = /home/coremake/ncbi/lib
XNCBI_ALTLIB = /home/coremake/ncbi/altlib
X#will work only when you have Motif installed!
XNCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF
XNCBI_VIBLIBS = -lXm -lXmu -lXp -lXpm -lXt -lX11 -lXext
XNCBI_DISTVIBLIBS = -L/usr/X11R6/lib /usr/X11R6/lib/libXm.a /usr/X11R6/lib/libXp.a /usr/X11R6/lib/libXpm.a -lXmu -lXt -lX11 -lXext
XNCBI_OTHERLIBS = -lm
XNCBI_RANLIB = ranlib
X# Used by makedis.csh
XNCBI_MT_OTHERLIBS =
XNCBI_THREAD_OBJ = ncbithr.o
XNETENTREZVERSION = 2.02c2ASN1SPEC6
END-of-ncbi.toolkit/files/freebsd.ncbi.mk
echo x - ncbi.toolkit/files/patch-aa
sed 's/^X//' >ncbi.toolkit/files/patch-aa << 'END-of-ncbi.toolkit/files/patch-aa'
X--- make/makeall.unx.orig Sat Jul 8 04:16:35 2000
X+++ make/makeall.unx Tue Oct 24 22:35:34 2000
X@@ -782,3 +782,174 @@
X #load $(LDFLAGS) getmuid.c medutil.c \
X $(SRC11) $(SRC8) $(SRC7) $(SRC6) $(SRC5) $(SRC3) \
X $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl
X+
X+EXE= Cn3Dv3d Nentrez Psequin \
X+ asn2fast asn2ff asndhuff asntool \
X+ bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \
X+ cdscan checksub copymat \
X+ ddv dosimple \
X+ entrcmd errhdr fa2htgs fastacmd findspl fmerge formatdb \
X+ getfeat getmesh getpub getseq gil2bin \
X+ idfetch impala indexpub \
X+ makemat makeset megablast \
X+ ncbisort netentcf \
X+ rpsblast \
X+ seedtop seqtest \
X+ tbl2asn testcore testobj testval \
X+ udv vecscreen
X+
X+
X+LIB= libncbi.a libncbicdr.a libncbimla.a libncbitxc2.a \
X+ libnetentr.a libncbiCacc.a libncbicn3d.a libncbimmdb.a \
X+ libnetblast.a libvibgif.a libncbiNacc.a libncbidesk.a \
X+ libncbiobj.a libnetcli.a libvibnet.a libncbiacc.a \
X+ libncbiid1.a libncbitool.a libnetcli_.a libvibrant.a
X+
X+
X+INC= actutils.h matrix.h rpsutil.h \
X+ asnblock.h mbalign.h saldist.h \
X+ asncode.h mblast.h saled.h \
X+ asnent2.h mbutils.h saledit.h \
X+ asnfdef.h mconsist.h salfiles.h \
X+ asnfeat.h mdrcherr.h salign.h \
X+ asngen.h medarch.h salmedia.h \
X+ asnid0.h medutil.h salogif.h \
X+ asnloc.h medview.h salpacc.h \
X+ asnmdrs.h mkbioseq.h salpanel.h \
X+ asnmedli.h mmdb1.h salparam.h \
X+ asnmime.h mmdb2.h salpedit.h \
X+ asnmla.h mmdb3.h salprop.h \
X+ asnneten.h mmdbapi.h salpstat.h \
X+ asnproj.h mmdbapi1.h salptool.h \
X+ asnprt.h mmdbapi2.h salsa.h \
X+ asnpub.h mmdbapi3.h salsap.h \
X+ asnpubme.h mmdbapi4.h salstruc.h \
X+ asnres.h mmdbdata.h salutil.h \
X+ asnseq.h mmdblocl.h samutil.h \
X+ asnsset.h ncbi.h satutil.h \
X+ asnsubmt.h ncbibs.h sdisplay.h \
X+ asntax1.h ncbibuf.h sec.h \
X+ asntaxon.h ncbicli.h seed.h \
X+ bandalgn.h ncbidraw.h seg.h \
X+ binary.h ncbienv.h seqanal.h \
X+ biosrc.h ncbierr.h seqcons.h \
X+ blast.h ncbifile.h seqfltr.h \
X+ blastdef.h ncbigif.h seqgraph.h \
X+ blastkar.h ncbilang.h seqgrphx.h \
X+ blastpat.h ncbilcl.h seqmgr.h \
X+ blastpri.h ncbimain.h seqmtrx.h \
X+ blocks.h ncbimath.h seqpcc.h \
X+ blstspc.h ncbimem.h seqport.h \
X+ bspview.h ncbimisc.h seqscrl.h \
X+ casn.h ncbimsg.h seqsub.h \
X+ cdconfig.h ncbinet.h sequtil.h \
X+ cdd.h ncbiopt.h shim3d.h \
X+ cdentrez.h ncbiport.h simple.h \
X+ cdnewlib.h ncbiprop.h simutil.h \
X+ cdrgn.h ncbisam.h spell.h \
X+ cdrom.h ncbisami.h splutil.h \
X+ cdromlib.h ncbisgml.h sqnutils.h \
X+ cn3dentr.h ncbisock.h strimprt.h \
X+ cn3dmain.h ncbisort.h stsutil.h \
X+ cn3dmesh.h ncbisrti.h subutil.h \
X+ cn3dmodl.h ncbistd.h suggapi.h \
X+ cn3dmsel.h ncbistr.h suggen.h \
X+ cn3dmsg.h ncbithr.h suggest.h \
X+ cn3dopen.h ncbitime.h suggslp.h \
X+ cn3dsave.h ncbiurl.h sugmap.h \
X+ cn3dshim.h ncbiwin.h sugprefx.h \
X+ cn3dstyl.h ncbiwww.h tax0.h \
X+ cn3dxprt.h netblap3.h tax1map.h \
X+ codon.h netcnfg.h taxblast.h \
X+ con_file.h netentr.h taxext.h \
X+ con_sock.h netlib.h taxinc.h \
X+ con_stateless.h netpriv.h taxon1.h \
X+ con_url.h netscape.h taxuerr.h \
X+ ni_asn.h taxutil.h \
X+ connectn.h ni_defin.h terr.h \
X+ connectr.h ni_encr.h tfuns.h \
X+ connutil.h ni_error.h toasn3.h \
X+ corematx.h ni_lib.h tofasta.h \
X+ db_list.h ni_lib_.h tofile.h \
X+ ddvclick.h ni_list.h tomedlin.h \
X+ ddvcolor.h ni_msg.h toporg.h \
X+ ddvcreate.h ni_net.h tree.h \
X+ ddvgraph.h ni_types.h treemgr.h \
X+ ddvmain.h objacces.h treeview.h \
X+ ddvopen.h objalign.h treevint.h \
X+ ddvpanel.h objalignloc.h tsprintf.h \
X+ diagnost.h objall.h txalign.h \
X+ dlogutil.h objbibli.h txclient.h \
X+ document.h objblock.h txcommon.h \
X+ dotmatrx.h objblst3.h udvdef.h \
X+ drawingp.h objcdd.h udviewer.h \
X+ drawseq.h objcode.h udvseq.h \
X+ dust.h objent2.h undefwin.h \
X+ dvncode.h objentr.h urkbias.h \
X+ echo_asn.h objfdef.h urkcnsrt.h \
X+ edutil.h objfeat.h urkdust.h \
X+ ent2api.h objgen.h urkepi.h \
X+ entrez.h objloc.h urkfltr.h \
X+ errdefn.h objmdrs.h urkgraph.h \
X+ explore.h objmedli.h urkpcc.h \
X+ fea2seg.h objmgr.h urkptpf.h \
X+ ffprint.h objmime.h urksigu.h \
X+ findrepl.h objmla.h urktree.h \
X+ fstyle.h objmmdb1.h urkutil.h \
X+ fstylep.h objmmdb2.h urlquery.h \
X+ ftusrstr.h objmmdb3.h utilpars.h \
X+ gapxdrop.h objneten.h utilpub.h \
X+ gather.h objproj.h valid.h \
X+ gbfeat.h objprt.h validatr.h \
X+ gbftdef.h objpub.h validerr.h \
X+ gbparlex.h objpubd.h vast2cn3d.h \
X+ gifgen.h objpubme.h vast2mage.h \
X+ glbpic.h objres.h vast2pdb.h \
X+ gphdraw.h objseq.h vastlocl.h \
X+ gtrdraw.h objsset.h vastsrv.h \
X+ gxydraw.h objsub.h vecscnapi.h \
X+ id1.h objtax1.h vecscrn.h \
X+ id1arch.h objtaxc0.h vibdefns.h \
X+ id1gen.h odlbox.h vibfltr.h \
X+ id1map.h panels.h vibforms.h \
X+ image.h parsegb.h vibgraph.h \
X+ imagelst.h pdiagnos.h vibincld.h \
X+ import.h pgppop.h vibmouse.h \
X+ jzcoll.h pictur3d.h vibpcc.h \
X+ jzmisc.h picture.h vibprocs.h \
X+ layout.h picturep.h vibrant.h \
X+ lbapi.h pmfapi.h vibtree.h \
X+ legend.h pobutil.h vibtypes.h \
X+ list.h posit.h viewer.h \
X+ lnfac.h ppict3d.h viewer3d.h \
X+ lookup.h profiles.h viewerp.h \
X+ lsqfetch.h prtgene.h viewmgr.h \
X+ mapgene.h prtutil.h vsm.h \
X+ mapmime.h prunebsc.h vsmfile.h \
X+ mapmla.h pubdesc.h vsmpriv.h \
X+ mappingp.h puberr.h vsmutil.h \
X+ mapproj.h qblastapi.h wwwblast.h \
X+ mappubme.h readdb.h \
X+ maputil.h regex.h
X+
X+MKDIR= /bin/mkdir -p
X+INSTALL_PROGRAM= /usr/bin/install -c
X+
X+binstall: $(EXE)
X+ ${MKDIR} ${PREFIX}/bin
X+ ${INSTALL_PROGRAM} -s $? /${PREFIX}/bin
X+
X+linstall: $(LIB)
X+ ${MKDIR} ${PREFIX}/lib/ncbi
X+ ${INSTALL_PROGRAM} $? ${PREFIX}/lib/ncbi
X+
X+iinstall::
X+ ${MKDIR} ${PREFIX}/include/ncbi
X+ pwd
X+ cd ../include; \
X+ for file in $(INC); do \
X+ ${INSTALL_PROGRAM} $$file ${PREFIX}/include/ncbi; \
X+ done
X+
X+install: linstall binstall
X+
END-of-ncbi.toolkit/files/patch-aa
echo x - ncbi.toolkit/files/patch-ab
sed 's/^X//' >ncbi.toolkit/files/patch-ab << 'END-of-ncbi.toolkit/files/patch-ab'
X--- corelib/ncbilcl.bsd.orig Mon Apr 3 08:50:57 2000
X+++ corelib/ncbilcl.bsd Mon Apr 3 08:51:55 2000
X@@ -74,7 +74,6 @@
X #include <stdio.h>
X #include <ctype.h>
X #include <string.h>
X-#include <malloc.h>
X #include <memory.h>
X #include <stdlib.h>
X #include <math.h>
X@@ -84,7 +83,7 @@
X
X /* Check if there are POSIX threads available */
X #ifdef _POSIX_THREADS
X-#define POSIX_THREADS_AVAIL
X+#define POSIX_THREADS_AVAIL_broken
X #endif
X
X
END-of-ncbi.toolkit/files/patch-ab
echo x - ncbi.toolkit/files/patch-ac
sed 's/^X//' >ncbi.toolkit/files/patch-ac << 'END-of-ncbi.toolkit/files/patch-ac'
X--- corelib/ncbienv.c.orig Tue Jan 25 08:16:49 2000
X+++ corelib/ncbienv.c Mon Apr 3 08:56:02 2000
X@@ -183,6 +183,8 @@
X
X #ifdef OS_UNIX
X #include <pwd.h>
X+#include <sys/param.h>
X+#define LOGNAME_MAX MAXLOGNAME
X #endif /* OS_UNIX */
X #ifdef OS_MAC
X #include <Gestalt.h>
END-of-ncbi.toolkit/files/patch-ac
echo x - ncbi.toolkit/distinfo
sed 's/^X//' >ncbi.toolkit/distinfo << 'END-of-ncbi.toolkit/distinfo'
XMD5 (ncbi/ncbi.tar.gz) = d201fc46e5e31e930ab73cc2dab79a2e
END-of-ncbi.toolkit/distinfo
echo x - ncbi.toolkit/Makefile
sed 's/^X//' >ncbi.toolkit/Makefile << 'END-of-ncbi.toolkit/Makefile'
X# New ports collection makefile for: NCBI
X# Date created: 03 April 2000
X# Whom: tonym
X#
X# $FreeBSD$
X#
X# View this file with tabstop=4
X#
X
XPORTNAME= ncbi.toolkit
XPORTVERSION= 2000.07.07
XCATEGORIES= biology
XMASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/
XDISTNAME= ncbi
XDIST_SUBDIR= ncbi
X
XMAINTAINER= tony.maher@ebioinformatics.com
X
XREQUIRES_MOTIF= yes
X
X#
X# In the files directory we have:
X#
X
XDUMMYMAKE= Makefile
X
X#
X# out of it for the post-install when we put in system startup file.
X#
X
XPLATFORMDIR= ${WRKSRC}/platform
XBUILDSCRIPT= ${WRKSRC}/make/makedis.csh
X
X#
X# Thus ends the definitions
X#
X
X#
X# We need a dummy top level Makefile as NCBI has scripts that need to
X# run from point above ncbi hierachy.
X#
X
Xpre-configure:
X @${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC}
X @${CP} ${FILESDIR}/freebsd.ncbi.mk ${PLATFORMDIR}
X @${PERL} -pi.orig -e 's#NetBSD#FreeBSD#;' -e 's#netbsd#freebsd#' ${BUILDSCRIPT}
X
X.include <bsd.port.mk>
END-of-ncbi.toolkit/Makefile
echo x - ncbi.toolkit/pkg-descr
sed 's/^X//' >ncbi.toolkit/pkg-descr << 'END-of-ncbi.toolkit/pkg-descr'
X"The NCBI Software Development Toolkit was developed for the production and
Xdistribution of GenBank, Entrez, BLAST, and related services by NCBI. We
Xmake it freely available to the public without restriction to facilitate the
Xuse of NCBI by the scientific community. However, please understand that
Xwhile we feel we have done a high quality job, this is not commercial
Xsoftware.
XThe documentation lags considerably behind the software and we must make any
Xchanges required by our data production needs. Nontheless, many people have
Xfound it a useful and stable basis for a number of tools and applications.
X
XThe toolkit is available by anonymous ftp from ncbi.nlm.nih.gov"
X
Xexcerpt from NCBI toolkit README file.
X
X-- Tony Maher <tony.maher@ebioinformatics.com>
X FreeBSD bio-porters <bio@freebsd.net>
END-of-ncbi.toolkit/pkg-descr
echo x - ncbi.toolkit/pkg-comment
sed 's/^X//' >ncbi.toolkit/pkg-comment << 'END-of-ncbi.toolkit/pkg-comment'
XNational Center for Biotechnology Information (NCBI) Development Toolkit.
END-of-ncbi.toolkit/pkg-comment
echo x - ncbi.toolkit/pkg-plist
sed 's/^X//' >ncbi.toolkit/pkg-plist << 'END-of-ncbi.toolkit/pkg-plist'
Xbin/Cn3Dv3d
Xbin/Nentrez
Xbin/Psequin
Xbin/asn2fast
Xbin/asn2ff
Xbin/asndhuff
Xbin/asntool
Xbin/bl2seq
Xbin/blast.REAL
Xbin/blastall
Xbin/blastcl3
Xbin/blastclust
Xbin/blastpgp
Xbin/cdscan
Xbin/checksub
Xbin/copymat
Xbin/ddv
Xbin/dosimple
Xbin/entrcmd
Xbin/errhdr
Xbin/fa2htgs
Xbin/fastacmd
Xbin/findspl
Xbin/fmerge
Xbin/formatdb
Xbin/getfeat
Xbin/getmesh
Xbin/getpub
Xbin/getseq
Xbin/gil2bin
Xbin/idfetch
Xbin/impala
Xbin/indexpub
Xbin/makemat
Xbin/makeset
Xbin/megablast
Xbin/ncbisort
Xbin/netentcf
Xbin/rpsblast
Xbin/seedtop
Xbin/seqtest
Xbin/tbl2asn
Xbin/testcore
Xbin/testobj
Xbin/testval
Xbin/udv
Xbin/vecscreen
Xlib/ncbi/libncbi.a
Xlib/ncbi/libncbicdr.a
Xlib/ncbi/libncbimla.a
Xlib/ncbi/libncbitxc2.a
Xlib/ncbi/libnetentr.a
Xlib/ncbi/libncbiCacc.a
Xlib/ncbi/libncbicn3d.a
Xlib/ncbi/libncbimmdb.a
Xlib/ncbi/libnetblast.a
Xlib/ncbi/libvibgif.a
Xlib/ncbi/libncbiNacc.a
Xlib/ncbi/libncbidesk.a
Xlib/ncbi/libncbiobj.a
Xlib/ncbi/libnetcli.a
Xlib/ncbi/libvibnet.a
Xlib/ncbi/libncbiacc.a
Xlib/ncbi/libncbiid1.a
Xlib/ncbi/libncbitool.a
Xlib/ncbi/libnetcli_.a
Xlib/ncbi/libvibrant.a
X@unexec rmdir %D/lib/ncbi
X@unexec rm -rf %D/include/ncbi
END-of-ncbi.toolkit/pkg-plist
exit
>Release-Note:
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