From 74b56bc3f6b32c8388c4986f292c7ba966211ff0 Mon Sep 17 00:00:00 2001 From: Pav Lucistnik Date: Mon, 1 Nov 2004 22:21:02 +0000 Subject: - Update to 2004.06.16 Inspired by: ports/72726 Approved by: maintainer timeout (2 weeks) --- biology/ncbi-toolkit/Makefile | 8 +- biology/ncbi-toolkit/distinfo | 3 +- biology/ncbi-toolkit/files/patch-aa | 12 +- biology/ncbi-toolkit/pkg-plist | 420 ++++++++++++++++++++++-------------- 4 files changed, 276 insertions(+), 167 deletions(-) (limited to 'biology') diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index 81be1572298b..c946237665c1 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -6,7 +6,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2003.04.21 +PORTVERSION= 2004.06.16 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -35,13 +35,13 @@ pre-configure: @${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC} post-install: - @${MKDIR} ${DATADIR} + ${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} ${DOCDIR} .endif @${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE} diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo index ee90dff3fe66..282f0acf867f 100644 --- a/biology/ncbi-toolkit/distinfo +++ b/biology/ncbi-toolkit/distinfo @@ -1 +1,2 @@ -MD5 (ncbi.tar.gz) = 96208e10f92b2163f5dcc3c5cf74dd44 +MD5 (ncbi.tar.gz) = 12320f853acb397a14729fb0da0b09df +SIZE (ncbi.tar.gz) = 13680457 diff --git a/biology/ncbi-toolkit/files/patch-aa b/biology/ncbi-toolkit/files/patch-aa index 8bb479ec9b0b..65458348ad2a 100644 --- a/biology/ncbi-toolkit/files/patch-aa +++ b/biology/ncbi-toolkit/files/patch-aa @@ -1,6 +1,6 @@ ---- make/makeall.unx.orig Thu Mar 21 06:01:20 2002 -+++ make/makeall.unx Sat Jun 8 20:16:09 2002 -@@ -859,3 +859,46 @@ +--- make/makeall.unx.orig Tue Jun 8 17:44:54 2004 ++++ make/makeall.unx Mon Nov 1 21:07:43 2004 +@@ -944,3 +944,48 @@ #load $(LDFLAGS) getmuid.c medutil.c \ $(SRC11) $(SRC8) $(SRC7) $(SRC6) $(SRC5) $(SRC3) \ $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl @@ -10,7 +10,7 @@ + blastall blastcl3 blastclust blastpgp \ + cdscan checksub copymat \ + ddv demo_regexp demo_regexp_grep dosimple \ -+ entrcmd entrez2 errhdr fa2htgs fastacmd findspl fmerge formatdb \ ++ entrcmd entrez2 errhdr fa2htgs fastacmd findspl formatdb \ + getfeat getmesh getpub getseq gil2bin \ + idfetch impala indexpub \ + makemat makeset megablast \ @@ -26,7 +26,9 @@ + +binstall: $(EXE) + ${MKDIR} ${PREFIX}/bin -+ ${INSTALL_PROGRAM} -s $? /${PREFIX}/bin ++.for f in $(EXE) ++ ${INSTALL_PROGRAM} -s $(f) ${PREFIX}/bin ++.endfor + +linstall: $(LIB) + ${MKDIR} ${PREFIX}/lib/ncbi diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist index d9cd41b1a767..08b9f8f2544d 100644 --- a/biology/ncbi-toolkit/pkg-plist +++ b/biology/ncbi-toolkit/pkg-plist @@ -1,51 +1,3 @@ -%%PORTDOCS%%%%DOCSDIR%%/FAQ.txt -%%PORTDOCS%%%%DOCSDIR%%/README-qm -%%PORTDOCS%%%%DOCSDIR%%/README.asn2xml -%%PORTDOCS%%%%DOCSDIR%%/README.bcl -%%PORTDOCS%%%%DOCSDIR%%/README.bls -%%PORTDOCS%%%%DOCSDIR%%/README.fastacmd -%%PORTDOCS%%%%DOCSDIR%%/README.formatdb -%%PORTDOCS%%%%DOCSDIR%%/README.imp -%%PORTDOCS%%%%DOCSDIR%%/README.mbl -%%PORTDOCS%%%%DOCSDIR%%/README.nbl -%%PORTDOCS%%%%DOCSDIR%%/README.pbl -%%PORTDOCS%%%%DOCSDIR%%/README.rps -%%PORTDOCS%%%%DOCSDIR%%/README.sdk -%%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt -%%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt -%%PORTDOCS%%%%DOCSDIR%%/dispatcher.html -%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README -%%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc -%%PORTDOCS%%%%DOCSDIR%%/firedialog.gif -%%PORTDOCS%%%%DOCSDIR%%/firewall.html -%%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh -%%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css -%%PORTDOCS%%%%DOCSDIR%%/images/seqn01.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn02.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn03.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn04.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn05.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn06.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn07.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn08.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn09.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn10.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn11.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn12.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn13.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn14.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn15.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn16.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn17.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn18.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn19.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn20.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn21.gif -%%PORTDOCS%%%%DOCSDIR%%/images/seqn22.gif -%%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt -%%PORTDOCS%%%%DOCSDIR%%/sdk.doc -%%PORTDOCS%%%%DOCSDIR%%/sequin.htm -%%PORTDOCS%%%%DOCSDIR%%/tbl2asn.txt bin/Nentrez bin/Psequin bin/asn2ff @@ -70,7 +22,6 @@ bin/errhdr bin/fa2htgs bin/fastacmd bin/findspl -bin/fmerge bin/formatdb bin/getfeat bin/getmesh @@ -94,56 +45,6 @@ bin/testobj bin/testval bin/udv bin/vecscreen -lib/ncbi/libddvlib.a -lib/ncbi/libncbi.a -lib/ncbi/libncbiCacc.a -lib/ncbi/libncbiNacc.a -lib/ncbi/libncbiacc.a -lib/ncbi/libncbicdr.a -lib/ncbi/libncbicn3d.a -lib/ncbi/libncbidesk.a -lib/ncbi/libncbiid1.a -lib/ncbi/libncbimla.a -lib/ncbi/libncbimmdb.a -lib/ncbi/libncbiobj.a -lib/ncbi/libncbitool.a -lib/ncbi/libncbitxc2.a -lib/ncbi/libnetblast.a -lib/ncbi/libnetcli.a -lib/ncbi/libnetentr.a -lib/ncbi/libregexp.a -lib/ncbi/libvibgif.a -lib/ncbi/libvibnet.a -lib/ncbi/libvibrant.a -include/ncbi/connect/connect_export.h -include/ncbi/connect/ncbi_ansi_ext.h -include/ncbi/connect/ncbi_buffer.h -include/ncbi/connect/ncbi_comm.h -include/ncbi/connect/ncbi_config.h -include/ncbi/connect/ncbi_connection.h -include/ncbi/connect/ncbi_connector.h -include/ncbi/connect/ncbi_connutil.h -include/ncbi/connect/ncbi_core.h -include/ncbi/connect/ncbi_core_c.h -include/ncbi/connect/ncbi_dispd.h -include/ncbi/connect/ncbi_file_connector.h -include/ncbi/connect/ncbi_heapmgr.h -include/ncbi/connect/ncbi_host_info.h -include/ncbi/connect/ncbi_host_infop.h -include/ncbi/connect/ncbi_http_connector.h -include/ncbi/connect/ncbi_lbsmd.h -include/ncbi/connect/ncbi_memory_connector.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 -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/FSpCompat.h include/ncbi/FullPath.h include/ncbi/MoreCarbonAccessors.h @@ -175,16 +76,12 @@ include/ncbi/asn2ff.h include/ncbi/asn2ff6.h include/ncbi/asn2ffg.h include/ncbi/asn2ffp.h +include/ncbi/asn2gnbi.h include/ncbi/asn2gnbk.h include/ncbi/asn2gnbp.h include/ncbi/asn2graphic.h include/ncbi/asn2graphicp.h include/ncbi/asnacces.h -include/ncbi/asngbseq.h -include/ncbi/asntseq.h -include/ncbi/blast.h -include/ncbi/blastconcat.h -include/ncbi/blastconcatdef.h include/ncbi/asnalign.h include/ncbi/asnbibli.h include/ncbi/asnblock.h @@ -192,8 +89,10 @@ include/ncbi/asncode.h include/ncbi/asnent2.h include/ncbi/asnfdef.h include/ncbi/asnfeat.h +include/ncbi/asngbseq.h include/ncbi/asngen.h include/ncbi/asnid0.h +include/ncbi/asninsdseq.h include/ncbi/asnloc.h include/ncbi/asnmdrs.h include/ncbi/asnmedli.h @@ -211,9 +110,13 @@ include/ncbi/asnsset.h include/ncbi/asnsubmt.h include/ncbi/asntax1.h include/ncbi/asntaxon.h +include/ncbi/asntseq.h include/ncbi/bandalgn.h include/ncbi/binary.h include/ncbi/biosrc.h +include/ncbi/blast.h +include/ncbi/blastconcat.h +include/ncbi/blastconcatdef.h include/ncbi/blastdef.h include/ncbi/blastkar.h include/ncbi/blastpat.h @@ -226,6 +129,7 @@ include/ncbi/bxmlobj.h include/ncbi/casn.h include/ncbi/cdconfig.h include/ncbi/cdd.h +include/ncbi/cddapi.h include/ncbi/cddposutil.h include/ncbi/cddsrv.h include/ncbi/cddutil.h @@ -247,6 +151,35 @@ include/ncbi/cn3dshim.h include/ncbi/cn3dstyl.h include/ncbi/cn3dxprt.h include/ncbi/codon.h +include/ncbi/connect/connect_export.h +include/ncbi/connect/ncbi_ansi_ext.h +include/ncbi/connect/ncbi_buffer.h +include/ncbi/connect/ncbi_comm.h +include/ncbi/connect/ncbi_config.h +include/ncbi/connect/ncbi_connection.h +include/ncbi/connect/ncbi_connector.h +include/ncbi/connect/ncbi_connutil.h +include/ncbi/connect/ncbi_core.h +include/ncbi/connect/ncbi_core_c.h +include/ncbi/connect/ncbi_dispd.h +include/ncbi/connect/ncbi_file_connector.h +include/ncbi/connect/ncbi_heapmgr.h +include/ncbi/connect/ncbi_host_info.h +include/ncbi/connect/ncbi_host_infop.h +include/ncbi/connect/ncbi_http_connector.h +include/ncbi/connect/ncbi_lbsmd.h +include/ncbi/connect/ncbi_memory_connector.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 +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/corematx.h include/ncbi/db_list.h include/ncbi/ddvclick.h @@ -262,9 +195,9 @@ include/ncbi/document.h include/ncbi/dotmatrx.h include/ncbi/dotseq.h include/ncbi/dotviewer.h -include/ncbi/dust.h include/ncbi/drawingp.h include/ncbi/drawseq.h +include/ncbi/dust.h include/ncbi/dvncode.h include/ncbi/echo_asn.h include/ncbi/edutil.h @@ -296,6 +229,10 @@ include/ncbi/id1.h include/ncbi/id1arch.h include/ncbi/id1gen.h include/ncbi/id1map.h +include/ncbi/id2.h +include/ncbi/id2gen.h +include/ncbi/id2map.h +include/ncbi/id2sgen.h include/ncbi/image.h include/ncbi/imagelst.h include/ncbi/import.h @@ -407,6 +344,7 @@ include/ncbi/objfdef.h include/ncbi/objfeat.h include/ncbi/objgbseq.h include/ncbi/objgen.h +include/ncbi/objinsdseq.h include/ncbi/objloc.h include/ncbi/objmdrs.h include/ncbi/objmedli.h @@ -424,7 +362,9 @@ include/ncbi/objpub.h include/ncbi/objpubd.h include/ncbi/objpubme.h include/ncbi/objres.h +include/ncbi/objscoremat.h include/ncbi/objseq.h +include/ncbi/objspell.h include/ncbi/objsset.h include/ncbi/objsub.h include/ncbi/objtax1.h @@ -452,8 +392,8 @@ include/ncbi/prunebsc.h include/ncbi/pubdesc.h include/ncbi/puberr.h include/ncbi/qblastapi.h -include/ncbi/regex.h include/ncbi/readdb.h +include/ncbi/regex.h include/ncbi/rpsutil.h include/ncbi/saldist.h include/ncbi/saled.h @@ -475,6 +415,7 @@ include/ncbi/salstruc.h include/ncbi/salutil.h include/ncbi/samutil.h include/ncbi/satutil.h +include/ncbi/scoremat.h include/ncbi/sdisplay.h include/ncbi/sec.h include/ncbi/seed.h @@ -490,12 +431,14 @@ include/ncbi/seqpanel.h include/ncbi/seqpcc.h include/ncbi/seqport.h include/ncbi/seqscrl.h +include/ncbi/seqsplit.h include/ncbi/seqsub.h include/ncbi/sequtil.h include/ncbi/shim3d.h include/ncbi/simple.h include/ncbi/simutil.h include/ncbi/spell.h +include/ncbi/spellapi.h include/ncbi/spidey.h include/ncbi/splutil.h include/ncbi/sqnutils.h @@ -506,7 +449,6 @@ include/ncbi/subutil.h include/ncbi/suggapi.h include/ncbi/suggen.h include/ncbi/suggest.h -include/ncbi/terr.h include/ncbi/suggslp.h include/ncbi/sugmap.h include/ncbi/sugprefx.h @@ -517,6 +459,7 @@ include/ncbi/taxinc.h include/ncbi/taxon1.h include/ncbi/taxuerr.h include/ncbi/taxutil.h +include/ncbi/terr.h include/ncbi/tfuns.h include/ncbi/thrdatd.h include/ncbi/thrddecl.h @@ -558,7 +501,6 @@ include/ncbi/vast2cn3d.h include/ncbi/vast2mage.h include/ncbi/vast2pdb.h include/ncbi/vastlocl.h -include/ncbi/vsm.h include/ncbi/vastsrv.h include/ncbi/vecscnapi.h include/ncbi/vecscrn.h @@ -571,67 +513,231 @@ include/ncbi/vibmouse.h include/ncbi/vibpcc.h include/ncbi/vibprocs.h include/ncbi/vibrant.h +include/ncbi/vibrgb.h include/ncbi/vibtree.h include/ncbi/vibtypes.h include/ncbi/viewer.h include/ncbi/viewer3d.h include/ncbi/viewerp.h include/ncbi/viewmgr.h +include/ncbi/vsm.h include/ncbi/vsmfile.h include/ncbi/vsmpriv.h include/ncbi/vsmutil.h include/ncbi/wrpsb.h 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 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