Date: Fri, 22 Feb 2002 16:56:21 +1100 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/35203: Maintainer update: biology/ncbi-toolkit Message-ID: <200202220556.g1M5uLF83378@c31516.thorn1.nsw.optusnet.com.au>
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>Number: 35203 >Category: ports >Synopsis: Maintainer update: biology/ncbi-toolkit >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Thu Feb 21 22:00:02 PST 2002 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.5-STABLE i386 >Organization: BioLateral >Environment: System: FreeBSD dt.home 4.5-STABLE FreeBSD 4.5-STABLE #0: Fri Feb 22 12:29:39 EST 2002 root@dt.home:/usr/obj/usr/src/sys/DT i386 >Description: Maintainer update: biology/ncbi-toolkit Update from version 2001.04.03 to 2001.12.20 (and reset port revision) Also now install the ncbi "data" files that allow you to run protein blast searches. Previously I didn't do that (as I was only testing nucleotide blast search). Add in pkg-message to remind users that they need to create .ncbirc in order to use the data files. >How-To-Repeat: >Fix: diff -ruN ncbi-toolkit.orig/Makefile ncbi-toolkit/Makefile --- ncbi-toolkit.orig/Makefile Wed Sep 19 23:03:17 2001 +++ ncbi-toolkit/Makefile Fri Feb 22 16:17:28 2002 @@ -6,8 +6,8 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2001.04.03 -PORTREVISION= 1 +PORTVERSION= 2001.12.20 +PORTREVISION= 0 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -21,11 +21,6 @@ # DUMMYMAKE= Makefile - -# -# out of it for the post-install when we put in system startup file. -# - PLATFORMDIR= ${WRKSRC}/platform BUILDSCRIPT= ${WRKSRC}/make/makedis.csh @@ -33,11 +28,9 @@ CPIO= cpio --quiet -pdum -R # -# Thus ends the definitions -# - +# Thus ends the definitions. # -# We need a dummy top level Makefile as NCBI has scripts that need to +# Now we need a dummy top level Makefile as NCBI has scripts that need to # run from point above ncbi hierachy. # @@ -47,10 +40,17 @@ @${PERL} -pi.orig -e 's#NetBSD#FreeBSD#;' -e 's#netbsd#freebsd#' ${BUILDSCRIPT} post-install: + @${MKDIR} ${DATADIR} + @for file in ${WRKSRC}/data/*; do \ + ${INSTALL_DATA} $$file ${DATADIR}; \ + done .if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCDIR} - @ cd ${WRKSRC}/doc && find * | \ + @${MKDIR} ${DOCDIR} + @cd ${WRKSRC}/doc && find * | \ ${CPIO} ${SHAREOWN}:${SHAREGRP} ${DOCDIR} +.endif +.if !defined(BATCH) + @ ${CAT} ${PKGMESSAGE} | ${SED} -e "s#%%PREFIX%%#${PREFIX}#" .endif .include <bsd.port.mk> diff -ruN ncbi-toolkit.orig/distinfo ncbi-toolkit/distinfo --- ncbi-toolkit.orig/distinfo Thu Jun 21 00:25:54 2001 +++ ncbi-toolkit/distinfo Tue Feb 19 20:26:52 2002 @@ -1 +1 @@ -MD5 (ncbi.tar.gz) = 7bbfecf047f4e43c4e7bc292865c3485 +MD5 (ncbi.tar.gz) = 8038afb3f5502b3b8ade4f221eebe46e diff -ruN ncbi-toolkit.orig/files/freebsd.ncbi.mk ncbi-toolkit/files/freebsd.ncbi.mk --- ncbi-toolkit.orig/files/freebsd.ncbi.mk Mon Oct 30 00:56:24 2000 +++ ncbi-toolkit/files/freebsd.ncbi.mk Tue Feb 19 21:30:18 2002 @@ -25,3 +25,7 @@ NCBI_MT_OTHERLIBS = NCBI_THREAD_OBJ = ncbithr.o NETENTREZVERSION = 2.02c2ASN1SPEC6 + +NCBI_LBSM_SRC = ncbi_service_lbsmd_stub.c +NCBI_LBSM_OBJ = ncbi_service_lbsmd_stub.o + diff -ruN ncbi-toolkit.orig/files/patch-aa ncbi-toolkit/files/patch-aa --- ncbi-toolkit.orig/files/patch-aa Tue Sep 18 16:19:30 2001 +++ ncbi-toolkit/files/patch-aa Fri Feb 22 15:22:51 2002 @@ -6,7 +6,7 @@ $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl + +EXE= Nentrez Psequin \ -+ asn2fast asn2ff asndhuff asntool \ ++ asn2fast asn2ff asn2xml asndhuff asntool \ + bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \ + cdscan checksub copymat \ + ddv dosimple \ diff -ruN ncbi-toolkit.orig/pkg-message ncbi-toolkit/pkg-message --- ncbi-toolkit.orig/pkg-message Thu Jan 1 10:00:00 1970 +++ ncbi-toolkit/pkg-message Fri Feb 22 16:11:38 2002 @@ -0,0 +1,6 @@ +The data files are installed in "%%PREFIX%%/share/ncbi-tookit". +To use them you need to create a .ncbirc file in your home directory +with the following lines: + +[NCBI] +Data=%%PREFIX%%/share/ncbi-toolkit/ diff -ruN ncbi-toolkit.orig/pkg-plist ncbi-toolkit/pkg-plist --- ncbi-toolkit.orig/pkg-plist Tue Sep 18 16:19:40 2001 +++ ncbi-toolkit/pkg-plist Fri Feb 22 15:25:26 2002 @@ -44,6 +44,7 @@ bin/Psequin bin/asn2fast bin/asn2ff +bin/asn2xml bin/asndhuff bin/asntool bin/bl2seq @@ -116,11 +117,10 @@ include/ncbi/connect/ncbi_file_connector.h include/ncbi/connect/ncbi_heapmgr.h include/ncbi/connect/ncbi_http_connector.h -include/ncbi/connect/ncbi_lbsm.h -include/ncbi/connect/ncbi_lbsm_ipc.h include/ncbi/connect/ncbi_priv.h include/ncbi/connect/ncbi_sendmail.h include/ncbi/connect/ncbi_server_info.h +include/ncbi/connect/ncbi_server_infop.h include/ncbi/connect/ncbi_service.h include/ncbi/connect/ncbi_service_connector.h include/ncbi/connect/ncbi_servicep.h @@ -128,6 +128,7 @@ include/ncbi/connect/ncbi_servicep_lbsmd.h include/ncbi/connect/ncbi_socket.h include/ncbi/connect/ncbi_socket_connector.h +include/ncbi/connect/ncbi_types.h include/ncbi/connect/ncbi_util.h include/ncbi/PubStructAsn.h include/ncbi/a2ferr.h @@ -141,7 +142,10 @@ include/ncbi/algorend.h include/ncbi/alignloc.h include/ncbi/alignmgr.h +include/ncbi/alignmgr2.h include/ncbi/alignval.h +include/ncbi/aliparse.h +include/ncbi/aliread.h include/ncbi/all.h include/ncbi/allpub.h include/ncbi/apparam.h @@ -151,6 +155,9 @@ include/ncbi/asn2ffg.h include/ncbi/asn2ffp.h include/ncbi/asn2gnbk.h +include/ncbi/asn2gnbp.h +include/ncbi/asn2graphic.h +include/ncbi/asn2graphicp.h include/ncbi/asnacces.h include/ncbi/blast.h include/ncbi/asnalign.h @@ -202,6 +209,7 @@ include/ncbi/cdrgn.h include/ncbi/cdrom.h include/ncbi/cdromlib.h +include/ncbi/cn3d.h include/ncbi/cn3dentr.h include/ncbi/cn3dmain.h include/ncbi/cn3dmesh.h @@ -237,6 +245,7 @@ include/ncbi/edutil.h include/ncbi/ent2api.h include/ncbi/entrez.h +include/ncbi/entrez2.h include/ncbi/errdefn.h include/ncbi/explore.h include/ncbi/fastadl.h @@ -265,6 +274,9 @@ include/ncbi/image.h include/ncbi/imagelst.h include/ncbi/import.h +include/ncbi/ingenext.h +include/ncbi/ingengraph.h +include/ncbi/ingenwin.h include/ncbi/jsavlt.h include/ncbi/jzcoll.h include/ncbi/jzmisc.h @@ -275,6 +287,7 @@ include/ncbi/lnfac.h include/ncbi/lookup.h include/ncbi/lsqfetch.h +include/ncbi/mapcn3d.h include/ncbi/mapgene.h include/ncbi/mapmime.h include/ncbi/mapmla.h @@ -285,7 +298,6 @@ include/ncbi/matrix.h include/ncbi/mbalign.h include/ncbi/mblast.h -include/ncbi/mbutils.h include/ncbi/mconsist.h include/ncbi/mdrcherr.h include/ncbi/medarch.h @@ -303,6 +315,7 @@ include/ncbi/mmdbapi4.h include/ncbi/mmdbdata.h include/ncbi/mmdblocl.h +include/ncbi/motif.h include/ncbi/ncbi.h include/ncbi/ncbibs.h include/ncbi/ncbibuf.h @@ -361,6 +374,7 @@ include/ncbi/objblock.h include/ncbi/objblst3.h include/ncbi/objcdd.h +include/ncbi/objcn3d.h include/ncbi/objcode.h include/ncbi/objent2.h include/ncbi/objentr.h @@ -450,6 +464,7 @@ include/ncbi/simple.h include/ncbi/simutil.h include/ncbi/spell.h +include/ncbi/spidey.h include/ncbi/splutil.h include/ncbi/sqnutils.h include/ncbi/strimprt.h @@ -537,9 +552,55 @@ include/ncbi/wrpsbtool.h include/ncbi/wwwblast.h include/ncbi/xmlblast.h +share/ncbi-toolkit/BLOSUM45 +share/ncbi-toolkit/BLOSUM62 +share/ncbi-toolkit/BLOSUM80 +share/ncbi-toolkit/ContactPotential +share/ncbi-toolkit/KSat.flt +share/ncbi-toolkit/KSchoth.flt +share/ncbi-toolkit/KSesigc.mat +share/ncbi-toolkit/KSesigl.mat +share/ncbi-toolkit/KSgc.flt +share/ncbi-toolkit/KShopp.flt +share/ncbi-toolkit/KSkyte.flt +share/ncbi-toolkit/KSmtidk.mat +share/ncbi-toolkit/KSmtk.mat +share/ncbi-toolkit/KSnsigc.mat +share/ncbi-toolkit/KSnsigl.mat +share/ncbi-toolkit/KSpcc.mat +share/ncbi-toolkit/KSpsigc.mat +share/ncbi-toolkit/KSpsigl.mat +share/ncbi-toolkit/KSpur.flt +share/ncbi-toolkit/KSpyr.flt +share/ncbi-toolkit/PAM30 +share/ncbi-toolkit/PAM70 +share/ncbi-toolkit/asn2ff.prt +share/ncbi-toolkit/blast.prt +share/ncbi-toolkit/bstdt.prt +share/ncbi-toolkit/bstdt.val +share/ncbi-toolkit/featdef.prt +share/ncbi-toolkit/featdef.val +share/ncbi-toolkit/gc.prt +share/ncbi-toolkit/gc.val +share/ncbi-toolkit/humrep.fsa +share/ncbi-toolkit/lineages.txt +share/ncbi-toolkit/makerpt.prt +share/ncbi-toolkit/ncbiendo.dat +share/ncbi-toolkit/ncbipnam.dat +share/ncbi-toolkit/ncbipros.dat +share/ncbi-toolkit/ncbiren.dat +share/ncbi-toolkit/ncbirnam.dat +share/ncbi-toolkit/objprt.prt +share/ncbi-toolkit/pubkey.enc +share/ncbi-toolkit/seqcode.prt +share/ncbi-toolkit/seqcode.val +share/ncbi-toolkit/sequin.hlp +share/ncbi-toolkit/sgmlbb.ent +share/ncbi-toolkit/taxlist.txt @dirrm include/ncbi/connect @dirrm include/ncbi @dirrm lib/ncbi +@dirrm share/ncbi-toolkit %%PORTDOCS%%@dirrm share/doc/ncbi-toolkit/images %%PORTDOCS%%@dirrm share/doc/ncbi-toolkit/fa2htgs %%PORTDOCS%%@dirrm share/doc/ncbi-toolkit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with 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