diff options
Diffstat (limited to 'biology/ncbi-toolkit')
| -rw-r--r-- | biology/ncbi-toolkit/Makefile | 87 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/distinfo | 4 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c | 11 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-make-makenet.unx | 16 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-descr | 2 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-plist | 244 |
6 files changed, 173 insertions, 191 deletions
diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index aefb42e3cd67..3c1ef4e2cf66 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -2,18 +2,20 @@ # $FreeBSD$ PORTNAME= ncbi-toolkit -PORTVERSION= 2009.03.01 # containing BLAST v2.2.19 -PORTREVISION= 1 +PORTVERSION= 2012.06.20 # containing BLAST v2.2.27 CATEGORIES= biology -MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ +MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support +OPTIONS_DEFINE= DOCS + USE_MOTIF= yes -CPIO_ARGS= --quiet -pdum -R +MAKE_JOBS_UNSAFE= yes + SUB_FILES= pkg-message # These are the executables we install. @@ -28,32 +30,42 @@ SUB_FILES= pkg-message # change in the future with the addition of selectable knobs or # new slave ports -TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \ - debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \ - idfetch indexpub makeset tbl2asn vecscreen demo_regexp \ - demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp +TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \ + checksub debruijn demo_regexp demo_regexp_grep dosimple \ + entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \ + gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \ + vecscreen BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \ fastacmd formatdb formatrpsdb impala makemat megablast \ rpsblast seedtop taxblast X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv # and these are the man pages we have -MAN1= Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \ - asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \ - cdscan.1 checksub.1 copymat.1 ddv.1 \ - debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \ - fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \ - idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \ - tbl2asn.1 udv.1 vecscreen.1 - -MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \ - blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \ - blast.1 seedtop.1 blast.1 rpsblast.1 +MAN1= Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \ + asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \ + copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \ + fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \ + getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \ + taxblast.1 tbl2asn.1 udv.1 vecscreen.1 + +MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \ + blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \ + blast.1 seedtop.1 blast.1 rpsblast.1 + +.include <bsd.port.options.mk> post-patch: - @${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \ - ${WRKSRC}/make/makedis.csh \ - ${WRKSRC}/platform/freebsd.ncbi.mk + @${REINPLACE_CMD} -e \ + 's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh + @${REINPLACE_CMD} -e \ + '/^NCBI_CC/s|=.*|= ${CC}| ; \ + /^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \ + /^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \ + s|-I/usr/X11R6/include||g ; \ + s|-L/usr/X11R6/lib||g ; \ + s|/usr/local|${LOCALBASE}|g ; \ + s|-Wl,-Bstatic|| ; \ + s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk # the ncbi-toolkit provides a shell script to drive the build # and we use it @@ -68,36 +80,33 @@ do-install: .for blastexe in ${BLAST_EXE} (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin) .endfor - .for toolkitexe in ${TOOLKIT_EXE} (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin) .endfor - .for x11exe in ${X11_EXE} (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin) .endfor - @${MKDIR} ${PREFIX}/lib/${DISTNAME} (cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME}) + @${MKDIR} ${PREFIX}/include/${DISTNAME} + (cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \ + ${PREFIX}/include/${DISTNAME}) @${MKDIR} ${PREFIX}/include/${DISTNAME}/connect - (cd ${WRKSRC}/include && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}) - (cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}/connect) - + (cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \ + ${PREFIX}/include/${DISTNAME}/connect) .for man in ${MAN1} - (cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1) + (cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${MANPREFIX}/man/man1) .endfor - -post-install: @${MKDIR} ${DATADIR} - (cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR}) - -.if !defined(NOPORTDOCS) + (cd ${WRKSRC}/data && ${INSTALL_DATA} * ${DATADIR}) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} - (cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR}) -.endif - -.if !defined(BATCH) - @ ${CAT} ${PKGMESSAGE} + @(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \ + (cd ${DOCSDIR} && ${TAR} --unlink -xf -) + @${FIND} ${DOCSDIR} | ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP} + @${FIND} ${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx + @${FIND} ${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE} .endif + @${CAT} ${PKGMESSAGE} .include <bsd.port.mk> diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo index c5dfce97e894..8b767a5e8fd1 100644 --- a/biology/ncbi-toolkit/distinfo +++ b/biology/ncbi-toolkit/distinfo @@ -1,2 +1,2 @@ -SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df -SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732 +SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c +SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744 diff --git a/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c b/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c new file mode 100644 index 000000000000..095c6231ba55 --- /dev/null +++ b/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c @@ -0,0 +1,11 @@ +--- corelib/ncbimisc.c.orig ++++ corelib/ncbimisc.c +@@ -1266,7 +1266,7 @@ + if (len < 1) return NULL; + + rsult = (Nlm_CharPtr) MemNew (len + 3); +- if (rsult == NULL) return; ++ if (rsult == NULL) return NULL; + tmp = rsult; + + for (i = 0; /* local [i] != NULL */ i < numitems; i++) { diff --git a/biology/ncbi-toolkit/files/patch-make-makenet.unx b/biology/ncbi-toolkit/files/patch-make-makenet.unx index 76d817d6c913..878c36e2abc9 100644 --- a/biology/ncbi-toolkit/files/patch-make-makenet.unx +++ b/biology/ncbi-toolkit/files/patch-make-makenet.unx @@ -8,7 +8,7 @@ SEQUIN_OPTS = LIBCOPY = cp -p SRCCOPY = ./ln-if-absent -@@ -923,17 +924,17 @@ +@@ -934,17 +935,17 @@ $(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \ $(LIBCOMPADJ) $(LIB2) $(LIB1) \ @@ -17,19 +17,19 @@ udv : $(OBJUDV) $(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ - $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \ + $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \ $(LIB23) $(LIBCOMPADJ) $(LIB2) \ - $(LIB1) $(VIBLIBS) $(OTHERLIBS) + $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) Nentrez : entrez.c $(ULIB31) $(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ -- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) -+ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) +- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) ++ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) # left this in (Tentrez) for script backwards compatibility Tentrez : entrez.c $(ULIB31) -@@ -1114,7 +1115,7 @@ +@@ -1140,7 +1141,7 @@ entrez2 : entrez2.c $(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \ $(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \ @@ -38,7 +38,7 @@ $(VIB_POST_LINK) entrez2 # demo program (spidey) -@@ -1383,7 +1384,7 @@ +@@ -1421,7 +1422,7 @@ $(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \ $(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \ $(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \ @@ -47,7 +47,7 @@ $(VIB_POST_LINK) Psequin # 'sbtedit' Submission Template Editor -@@ -1395,7 +1396,7 @@ +@@ -1433,7 +1434,7 @@ $(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \ $(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \ $(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \ @@ -55,4 +55,4 @@ + $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) $(VIB_POST_LINK) sbtedit - salogif.o: salogif.c + # 'streamer' Sequinesque Stream Editor diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr index 626926daca04..35331ba63d4d 100644 --- a/biology/ncbi-toolkit/pkg-descr +++ b/biology/ncbi-toolkit/pkg-descr @@ -16,4 +16,4 @@ From the README: have found it a useful and stable basis for a number of tools and applications. -WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml +WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist index 6804d8608983..6388a9c0dcb8 100644 --- a/biology/ncbi-toolkit/pkg-plist +++ b/biology/ncbi-toolkit/pkg-plist @@ -1,87 +1,51 @@ -bin/bl2seq -bin/blastall -bin/blastcl3 -bin/blastclust -bin/blastpgp -bin/copymat -bin/fastacmd -bin/formatdb -bin/formatrpsdb -bin/impala -bin/makemat -bin/megablast -bin/rpsblast -bin/seedtop -bin/taxblast +bin/Nentrez +bin/Psequin bin/asn2ff bin/asn2gb bin/asn2idx bin/asn2xml bin/asndhuff bin/asntool +bin/bl2seq +bin/blastall +bin/blastcl3 +bin/blastclust +bin/blastpgp +bin/cdscan bin/checksub +bin/copymat +bin/ddv bin/debruijn +bin/demo_regexp +bin/demo_regexp_grep +bin/dosimple bin/entrcmd +bin/entrez2 +bin/errhdr bin/fa2htgs +bin/fastacmd bin/findspl +bin/formatdb +bin/formatrpsdb +bin/gene2xml bin/getmesh bin/getpub -bin/ddv bin/gil2bin bin/idfetch +bin/impala bin/indexpub +bin/makemat bin/makeset -bin/tbl2asn -bin/vecscreen -bin/demo_regexp -bin/demo_regexp_grep -bin/errhdr -bin/gene2xml +bin/megablast bin/ncbisort -bin/seqtest -bin/test_regexp -bin/Nentrez -bin/Psequin -bin/entrez2 +bin/rpsblast bin/sbtedit +bin/seedtop +bin/seqtest +bin/taxblast +bin/tbl2asn bin/udv -include/ncbi/connect/connect_export.h -include/ncbi/connect/ncbi_ansi_ext.h -include/ncbi/connect/ncbi_assert.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_connssl.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_ftp_connector.h -include/ncbi/connect/ncbi_gnutls.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_lb.h -include/ncbi/connect/ncbi_lbsmd.h -include/ncbi/connect/ncbi_local.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_socket_unix.h -include/ncbi/connect/ncbi_socketp.h -include/ncbi/connect/ncbi_types.h -include/ncbi/connect/ncbi_util.h +bin/vecscreen include/ncbi/FSpCompat.h include/ncbi/FullPath.h include/ncbi/MoreCarbonAccessors.h @@ -155,6 +119,7 @@ include/ncbi/asntax1.h include/ncbi/asntax3.h include/ncbi/asntaxon.h include/ncbi/asntseq.h +include/ncbi/asnvalid.h include/ncbi/bandalgn.h include/ncbi/binary.h include/ncbi/biosrc.h @@ -185,7 +150,6 @@ include/ncbi/cdrom.h include/ncbi/cdromlib.h include/ncbi/cn3d.h include/ncbi/cn3dentr.h -include/ncbi/codon.h include/ncbi/cn3dmain.h include/ncbi/cn3dmesh.h include/ncbi/cn3dmodl.h @@ -196,10 +160,50 @@ include/ncbi/cn3dsave.h include/ncbi/cn3dshim.h include/ncbi/cn3dstyl.h include/ncbi/cn3dxprt.h +include/ncbi/codon.h include/ncbi/compo_heap.h include/ncbi/compo_mode_condition.h include/ncbi/composition_adjustment.h include/ncbi/composition_constants.h +include/ncbi/connect/connect_export.h +include/ncbi/connect/ncbi_ansi_ext.h +include/ncbi/connect/ncbi_assert.h +include/ncbi/connect/ncbi_base64.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_connssl.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_ftp_connector.h +include/ncbi/connect/ncbi_gnutls.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_lb.h +include/ncbi/connect/ncbi_lbsmd.h +include/ncbi/connect/ncbi_local.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_socket_unix.h +include/ncbi/connect/ncbi_socketp.h +include/ncbi/connect/ncbi_types.h +include/ncbi/connect/ncbi_util.h +include/ncbi/connect/ncbi_version.h include/ncbi/corematx.h include/ncbi/db_list.h include/ncbi/ddvclick.h @@ -240,12 +244,12 @@ include/ncbi/gather.h include/ncbi/gbfeat.h include/ncbi/gbftdef.h include/ncbi/gbparlex.h -include/ncbi/id1.h include/ncbi/gifgen.h include/ncbi/glbpic.h include/ncbi/gphdraw.h include/ncbi/gtrdraw.h include/ncbi/gxydraw.h +include/ncbi/id1.h include/ncbi/id1arch.h include/ncbi/id1gen.h include/ncbi/id1map.h @@ -289,9 +293,9 @@ include/ncbi/medutil.h include/ncbi/medview.h include/ncbi/mimapi.h include/ncbi/mkbioseq.h -include/ncbi/mmdb1.h include/ncbi/mla2api.h include/ncbi/mlkludge.h +include/ncbi/mmdb1.h include/ncbi/mmdb2.h include/ncbi/mmdb3.h include/ncbi/mmdbapi.h @@ -303,6 +307,7 @@ include/ncbi/mmdbdata.h include/ncbi/mmdblocl.h include/ncbi/motif.h include/ncbi/ncbi.h +include/ncbi/ncbi_skew_guard.h include/ncbi/ncbibs.h include/ncbi/ncbidraw.h include/ncbi/ncbienv.h @@ -338,11 +343,8 @@ include/ncbi/netentr.h include/ncbi/netlib.h include/ncbi/netpriv.h include/ncbi/netscape.h -include/ncbi/ni_defin.h include/ncbi/ni_error.h -include/ncbi/ni_lib.h include/ncbi/ni_lib_.h -include/ncbi/ni_net.h include/ncbi/ni_types.h include/ncbi/nlm_linear_algebra.h include/ncbi/objacces.h @@ -392,6 +394,7 @@ include/ncbi/objtable.h include/ncbi/objtax1.h include/ncbi/objtax3.h include/ncbi/objtseq.h +include/ncbi/objvalid.h include/ncbi/odlbox.h include/ncbi/optimize_target_freq.h include/ncbi/panels.h @@ -478,7 +481,6 @@ include/ncbi/suggen.h include/ncbi/suggest.h include/ncbi/suggslp.h include/ncbi/sugmap.h -include/ncbi/terr.h include/ncbi/sugprefx.h include/ncbi/tax1map.h include/ncbi/tax3api.h @@ -488,6 +490,7 @@ 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 @@ -523,6 +526,8 @@ include/ncbi/urkutil.h include/ncbi/urlquery.h include/ncbi/utilpars.h include/ncbi/utilpub.h +include/ncbi/valapi.h +include/ncbi/valdlg.h include/ncbi/valid.h include/ncbi/validatr.h include/ncbi/validerr.h @@ -531,7 +536,6 @@ include/ncbi/vast2mage.h include/ncbi/vast2pdb.h include/ncbi/vastlocl.h include/ncbi/vastsrv.h -include/ncbi/vsm.h include/ncbi/vecscnapi.h include/ncbi/vecscrn.h include/ncbi/vibdefns.h @@ -551,6 +555,7 @@ 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 @@ -586,10 +591,10 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/access.txt %%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt %%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt -%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html %%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html %%PORTDOCS%%%%DOCSDIR%%/blast/blast.html %%PORTDOCS%%%%DOCSDIR%%/blast/blastall.html +%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html %%PORTDOCS%%%%DOCSDIR%%/blast/blastdb.html %%PORTDOCS%%%%DOCSDIR%%/blast/blastftp.html %%PORTDOCS%%%%DOCSDIR%%/blast/blastpgp.html @@ -613,7 +618,6 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/firewall.html %%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh %%PORTDOCS%%%%DOCSDIR%%/gene2xml.txt -%%PORTDOCS%%%%DOCSDIR%%/images/logo.png %%PORTDOCS%%%%DOCSDIR%%/images/affil.png %%PORTDOCS%%%%DOCSDIR%%/images/annot.png %%PORTDOCS%%%%DOCSDIR%%/images/authors.png @@ -624,6 +628,7 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/images/genbank.png %%PORTDOCS%%%%DOCSDIR%%/images/graphic.png %%PORTDOCS%%%%DOCSDIR%%/images/loc_page.png +%%PORTDOCS%%%%DOCSDIR%%/images/logo.png %%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css %%PORTDOCS%%%%DOCSDIR%%/images/net_cfg.png %%PORTDOCS%%%%DOCSDIR%%/images/nucaln.png @@ -639,67 +644,11 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/images/update.png %%PORTDOCS%%%%DOCSDIR%%/images/validate.png %%PORTDOCS%%%%DOCSDIR%%/images/welcome.png -%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2all.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2fsa.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2idx.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asnval.1 -%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastall.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastall_old.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1 -%%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1 -%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1 -%%PORTDOCS%%%%DOCSDIR%%/man/cleanasn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/copymat.1 -%%PORTDOCS%%%%DOCSDIR%%/man/ddv.1 -%%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1 -%%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1 -%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1 -%%PORTDOCS%%%%DOCSDIR%%/man/fa2htgs.1 -%%PORTDOCS%%%%DOCSDIR%%/man/fastacmd.1 -%%PORTDOCS%%%%DOCSDIR%%/man/findspl.1 -%%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1 -%%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 -%%PORTDOCS%%%%DOCSDIR%%/man/formatrpsdb.1 -%%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1 -%%PORTDOCS%%%%DOCSDIR%%/man/gene2xml.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1 -%%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1 -%%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1 -%%PORTDOCS%%%%DOCSDIR%%/man/impala.1 -%%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1 -%%PORTDOCS%%%%DOCSDIR%%/man/insdseqget.1 -%%PORTDOCS%%%%DOCSDIR%%/man/makemat.1 -%%PORTDOCS%%%%DOCSDIR%%/man/makeset.1 -%%PORTDOCS%%%%DOCSDIR%%/man/megablast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/nps2gps.1 -%%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/sbtedit.1 -%%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1 -%%PORTDOCS%%%%DOCSDIR%%/man/sortbyquote.1 -%%PORTDOCS%%%%DOCSDIR%%/man/spidey.1 -%%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/trna2sap.1 -%%PORTDOCS%%%%DOCSDIR%%/man/trna2tbl.1 -%%PORTDOCS%%%%DOCSDIR%%/man/udv.1 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt %%PORTDOCS%%%%DOCSDIR%%/sdk.doc -%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/Makefile %%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif -%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css +%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.xml %%PORTDOCS%%%%DOCSDIR%%/seq_install/left.GIF %%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-ie.css @@ -709,12 +658,12 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.html %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.xml +%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.html %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.xml %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_install.html %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.html -%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.xml %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.html @@ -726,6 +675,7 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.html %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.xml %%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif +%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js %%PORTDOCS%%%%DOCSDIR%%/seq_install/spacer10.GIF %%PORTDOCS%%%%DOCSDIR%%/seq_install/template.xml %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie.css @@ -736,6 +686,12 @@ lib/ncbi/libvibrant.a %%DATADIR%%/16SCore.nhr %%DATADIR%%/16SCore.nin %%DATADIR%%/16SCore.nsq +%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nhr +%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nin +%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nsq +%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nhr +%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nin +%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nsq %%DATADIR%%/BLOSUM45 %%DATADIR%%/BLOSUM50 %%DATADIR%%/BLOSUM62 @@ -752,7 +708,6 @@ lib/ncbi/libvibrant.a %%DATADIR%%/KSchoth.flt %%DATADIR%%/KSesigc.mat %%DATADIR%%/KSesigl.mat -%%DATADIR%%/PAM250 %%DATADIR%%/KSgc.flt %%DATADIR%%/KShopp.flt %%DATADIR%%/KSkyte.flt @@ -768,6 +723,7 @@ lib/ncbi/libvibrant.a %%DATADIR%%/LSURef_93.fasta.nhr %%DATADIR%%/LSURef_93.fasta.nin %%DATADIR%%/LSURef_93.fasta.nsq +%%DATADIR%%/PAM250 %%DATADIR%%/PAM30 %%DATADIR%%/PAM70 %%DATADIR%%/SSURef_93.fasta.nhr @@ -780,6 +736,7 @@ lib/ncbi/libvibrant.a %%DATADIR%%/UniVec_Core.nin %%DATADIR%%/UniVec_Core.nsq %%DATADIR%%/asn2ff.prt +%%DATADIR%%/autofix.prt %%DATADIR%%/blast.prt %%DATADIR%%/bstdt.prt %%DATADIR%%/bstdt.val @@ -794,6 +751,9 @@ lib/ncbi/libvibrant.a %%DATADIR%%/gc.val %%DATADIR%%/humrep.fsa %%DATADIR%%/institution_codes.txt +%%DATADIR%%/lat_lon_country.txt +%%DATADIR%%/lat_lon_island.txt +%%DATADIR%%/lat_lon_water.txt %%DATADIR%%/lineages.txt %%DATADIR%%/makerpt.prt %%DATADIR%%/ncbiendo.dat @@ -802,6 +762,8 @@ lib/ncbi/libvibrant.a %%DATADIR%%/ncbiren.dat %%DATADIR%%/ncbirnam.dat %%DATADIR%%/objprt.prt +%%DATADIR%%/organelle_products.prt +%%DATADIR%%/product_rules.prt %%DATADIR%%/pubkey.enc %%DATADIR%%/rRNA_blast.nal %%DATADIR%%/rRNAstrand.nal @@ -810,13 +772,13 @@ lib/ncbi/libvibrant.a %%DATADIR%%/sequin.hlp %%DATADIR%%/sgmlbb.ent %%DATADIR%%/taxlist.txt -@dirrm include/ncbi/connect -@dirrm include/ncbi -@dirrm lib/ncbi -%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast -%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs -%%PORTDOCS%%@dirrm %%DOCSDIR%%/images -%%PORTDOCS%%@dirrm %%DOCSDIR%%/man +%%DATADIR%%/validrules.prt +@dirrmtry %%DATADIR%% %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install +%%PORTDOCS%%@dirrm %%DOCSDIR%%/images +%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs +%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast %%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrmtry %%DATADIR%% +@dirrm lib/ncbi +@dirrm include/ncbi/connect +@dirrm include/ncbi |