Date: Thu, 17 Mar 2005 21:40:10 GMT From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/67735: biology/ncbi-toolkit does not build bl2seq Message-ID: <200503172140.j2HLeAXt005854@freefall.freebsd.org>
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The following reply was made to PR ports/67735; it has been noted by GNATS. From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: Volker Stolz <vs@FreeBSD.org> Cc: FreeBSD GNATS PR Submission <freebsd-gnats-submit@FreeBSD.org> Subject: Re: ports/67735: biology/ncbi-toolkit does not build bl2seq Date: Thu, 17 Mar 2005 18:37:19 -0300 --PEIAKu/WMn1b1Hv9 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline +----[ Volker Stolz <vs@FreeBSD.org> (25.Jun.2004 16:43): | | Synopsis: biology/ncbi-toolkit does not build bl2seq | +----] Grrr, I forgot to add the patch. Here it is, Fernan --PEIAKu/WMn1b1Hv9 Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="ncbi-toolkit.diff" diff -ruN /usr/ports/biology/ncbi-toolkit/Makefile ncbi-toolkit/Makefile --- /usr/ports/biology/ncbi-toolkit/Makefile Mon Nov 8 13:04:37 2004 +++ ncbi-toolkit/Makefile Thu Mar 17 17:55:59 2005 @@ -1,3 +1,4 @@ +# ex:ts=8 # New ports collection makefile for: NCBI # Date created: 03 April 2000 # Whom: tonym @@ -6,44 +7,96 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2004.06.16 +PORTVERSION= 2004.10.20 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi +DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} -MAINTAINER= tonym@biolateral.com.au +MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support USE_MOTIF= yes +CPIO_ARGS= --quiet -pdum -R +PKGMESSAGE= ${WRKDIR}/pkg-message +# These are the executables we install. # -# In the files directory we have: -# - -DUMMYMAKE= Makefile -DOCDIR= ${PREFIX}/share/doc/${PORTNAME} -CPIO= cpio --quiet -pdum -R - -# -# Thus ends the definitions. -# -# Now 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} +# We follow Debian in the separation of the port in three +# main categories and in the selection of programs that +# are installed in each case. This Makes Sense (TM). +# Thus, we drop a handful of programs that are useful only as tests +# or code examples +# (credit goes to Aaron Ucko, the Debian maintainer of the NCBI stuff!) +# Right now the port installs all the executables below, this may +# change in the future with the addition of selectable knobs or +# new slave ports + +TOOLKIT_EXE= asn2ff asn2gb asn2xml asndhuff checksub debruijn \ + entrcmd fa2htgs findspl getseq getfeat getmesh \ + getpub gil2bin idfetch indexpub makeset tbl2asn vecscreen +BLAST_EXE= bl2seq blast blastall blastcl3 blastclust blastpgp copymat \ + fastacmd formatdb impala makemat megablast rpsblast seedtop +X11_EXE= Nentrez Psequin ddv entrez2 netentcf udv + +# and these are the man pages we have + +MAN1= Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \ + asntool.1 bl2seq.1 blast.1 blastall.1 blastcl3.1 blastclust.1 \ + blastpgp.1 cdscan.1 checksub.1 copymat.1 ddv.1 debruijn.1 entrcmd.1 \ + entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 fmerge.1 formatdb.1 \ + gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 idfetch.1 impala.1 \ + indexpub.1 makemat.1 makeset.1 megablast.1 netentcf.1 rpsblast.1 \ + seedtop.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 megablast.1 blast.1 seedtop.1 + +# the ncbi-toolkit provides a shell script to drive the build +# and we use it + +do-build: + cd ${WRKDIR}; ./${DISTNAME}/make/makedis.csh + +# the ncbi-toolkit does not provide an install target +# we thus roll our own + +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_PROGRAM} *.a ${PREFIX}/lib/${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) + +.for man in ${MAN1} + (cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1) +.endfor post-install: - ${MKDIR} ${DATADIR} - @for file in ${WRKSRC}/data/*; do \ - ${INSTALL_DATA} $$file ${DATADIR}; \ - done + @${MKDIR} ${DATADIR} + (cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR}) + .if !defined(NOPORTDOCS) - ${MKDIR} ${DOCDIR} - cd ${WRKSRC}/doc && ${FIND} * | \ - ${CPIO} ${SHAREOWN}:${SHAREGRP} ${DOCDIR} + @${MKDIR} ${DOCSDIR} + (cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR}) +.endif + +.if !defined(BATCH) + @ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${.CURDIR}/pkg-message > ${PKGMESSAGE} + @ ${CAT} ${PKGMESSAGE} .endif - @${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE} .include <bsd.port.mk> diff -ruN /usr/ports/biology/ncbi-toolkit/distinfo ncbi-toolkit/distinfo --- /usr/ports/biology/ncbi-toolkit/distinfo Mon Nov 8 13:04:37 2004 +++ ncbi-toolkit/distinfo Mon Jan 17 12:17:05 2005 @@ -1,2 +1,2 @@ -MD5 (ncbi.tar.gz) = 12320f853acb397a14729fb0da0b09df -SIZE (ncbi.tar.gz) = 13680457 +MD5 (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 3f82bce2a3ce549f055ff989a4b825ed +SIZE (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 13867811 diff -ruN /usr/ports/biology/ncbi-toolkit/files/Makefile ncbi-toolkit/files/Makefile --- /usr/ports/biology/ncbi-toolkit/files/Makefile Sun Oct 29 10:56:24 2000 +++ ncbi-toolkit/files/Makefile Wed Dec 31 21:00:00 1969 @@ -1,8 +0,0 @@ -# -# $FreeBSD: ports/biology/ncbi-toolkit/files/Makefile,v 1.1 2000/10/29 13:56:24 jeh Exp $ - -all: - cd ..; ./ncbi/make/makedis.csh - -install: - cd build; $(MAKE) install diff -ruN /usr/ports/biology/ncbi-toolkit/files/patch-aa ncbi-toolkit/files/patch-aa --- /usr/ports/biology/ncbi-toolkit/files/patch-aa Mon Nov 8 13:04:37 2004 +++ ncbi-toolkit/files/patch-aa Wed Dec 31 21:00:00 1969 @@ -1,51 +0,0 @@ ---- 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 -+ -+EXE= Nentrez Psequin \ -+ asn2ff asn2gb asn2xml asndhuff asntool \ -+ blastall blastcl3 blastclust blastpgp \ -+ cdscan checksub copymat \ -+ ddv demo_regexp demo_regexp_grep dosimple \ -+ entrcmd entrez2 errhdr fa2htgs fastacmd findspl formatdb \ -+ getfeat getmesh getpub getseq gil2bin \ -+ idfetch impala indexpub \ -+ makemat makeset megablast \ -+ ncbisort netentcf \ -+ rpsblast \ -+ seedtop seqtest \ -+ tbl2asn testcore testobj testval \ -+ udv vecscreen -+ -+ -+MKDIR= /bin/mkdir -p -+INSTALL_PROGRAM= /usr/bin/install -c -+ -+binstall: $(EXE) -+ ${MKDIR} ${PREFIX}/bin -+.for f in $(EXE) -+ ${INSTALL_PROGRAM} -s $(f) ${PREFIX}/bin -+.endfor -+ -+linstall: $(LIB) -+ ${MKDIR} ${PREFIX}/lib/ncbi -+ for file in *.a; do \ -+ ${INSTALL_PROGRAM} $$file ${PREFIX}/lib/ncbi; \ -+ done -+ -+iinstall:: -+ ${MKDIR} ${PREFIX}/include/ncbi/connect -+ cd ../include; \ -+ for file in *.h; do \ -+ ${INSTALL_PROGRAM} $$file ${PREFIX}/include/ncbi; \ -+ done -+ cd ../include/connect; \ -+ for file in *.h; do \ -+ ${INSTALL_PROGRAM} $$file ${PREFIX}/include/ncbi/connect; \ -+ done -+ -+install: iinstall linstall binstall -+ diff -ruN /usr/ports/biology/ncbi-toolkit/files/patch-bl2seq ncbi-toolkit/files/patch-bl2seq --- /usr/ports/biology/ncbi-toolkit/files/patch-bl2seq Tue Jun 8 17:23:06 2004 +++ ncbi-toolkit/files/patch-bl2seq Wed Dec 31 21:00:00 1969 @@ -1,12 +0,0 @@ ---- build/makefile.orig Tue Jun 8 17:21:49 2004 -+++ build/makefile Tue Jun 8 17:22:17 2004 -@@ -899,7 +899,8 @@ - rpsblast \ - seedtop seqtest \ - tbl2asn testcore testobj testval \ -- udv vecscreen -+ udv vecscreen \ -+ bl2seq - - - MKDIR= /bin/mkdir -p diff -ruN /usr/ports/biology/ncbi-toolkit/files/patch-ncbilcl.fbd ncbi-toolkit/files/patch-ncbilcl.fbd --- /usr/ports/biology/ncbi-toolkit/files/patch-ncbilcl.fbd Mon May 5 09:24:08 2003 +++ ncbi-toolkit/files/patch-ncbilcl.fbd Wed Dec 31 21:00:00 1969 @@ -1,18 +0,0 @@ ---- corelib/ncbilcl.fbd.orig Sat Nov 23 07:05:04 2002 -+++ corelib/ncbilcl.fbd Sat May 3 10:06:18 2003 -@@ -67,6 +67,7 @@ - /*----------------------------------------------------------------------*/ - #define SYSV_IPC_AVAIL /* System V Interprocess Communication available */ - #define _POSIX_C_SOURCE 199309L -+#define _XOPEN_SOURCE 600 /* req. for 5.0 */ - #define HAVE_STRCASECMP 1 - #define HAVE_STRDUP 1 - -@@ -87,6 +88,7 @@ - #include <errno.h> - #include <float.h> - #include <unistd.h> -+#include <sys/select.h> /* req. for 5.0. fd_set def. moved from types.h */ - - /* Check if there are POSIX threads available */ - #ifdef _POSIX_THREADS diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-plist ncbi-toolkit/pkg-plist --- /usr/ports/biology/ncbi-toolkit/pkg-plist Mon Nov 8 13:04:38 2004 +++ ncbi-toolkit/pkg-plist Thu Mar 17 17:54:31 2005 @@ -1,50 +1,71 @@ -bin/Nentrez -bin/Psequin -bin/asn2ff -bin/asn2gb -bin/asn2xml -bin/asndhuff -bin/asntool +bin/bl2seq +bin/blast bin/blastall bin/blastcl3 bin/blastclust bin/blastpgp -bin/cdscan -bin/checksub bin/copymat -bin/ddv -bin/demo_regexp -bin/demo_regexp_grep -bin/dosimple +bin/fastacmd +bin/formatdb +bin/impala +bin/makemat +bin/megablast +bin/rpsblast +bin/seedtop +bin/asn2ff +bin/asn2gb +bin/asn2xml +bin/asndhuff +bin/checksub +bin/debruijn bin/entrcmd -bin/entrez2 -bin/errhdr bin/fa2htgs -bin/fastacmd bin/findspl -bin/formatdb +bin/getseq bin/getfeat bin/getmesh bin/getpub -bin/getseq +bin/ddv 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 +bin/Nentrez +bin/Psequin +bin/entrez2 +bin/netentcf +bin/udv +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 @@ -109,6 +130,7 @@ include/ncbi/asnsset.h include/ncbi/asnsubmt.h include/ncbi/asntax1.h +include/ncbi/asntax3.h include/ncbi/asntaxon.h include/ncbi/asntseq.h include/ncbi/bandalgn.h @@ -121,6 +143,7 @@ include/ncbi/blastkar.h include/ncbi/blastpat.h include/ncbi/blastpri.h +include/ncbi/blfmtutl.h include/ncbi/blocks.h include/ncbi/blstspc.h include/ncbi/blstxml.h @@ -131,7 +154,6 @@ include/ncbi/cdd.h include/ncbi/cddapi.h include/ncbi/cddposutil.h -include/ncbi/cddsrv.h include/ncbi/cddutil.h include/ncbi/cdentrez.h include/ncbi/cdnewlib.h @@ -140,6 +162,7 @@ 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 @@ -150,36 +173,6 @@ 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 @@ -220,12 +213,12 @@ 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 @@ -243,7 +236,6 @@ include/ncbi/jzcoll.h include/ncbi/jzmisc.h include/ncbi/layout.h -include/ncbi/lbapi.h include/ncbi/legend.h include/ncbi/list.h include/ncbi/lnfac.h @@ -368,6 +360,7 @@ include/ncbi/objsset.h include/ncbi/objsub.h include/ncbi/objtax1.h +include/ncbi/objtax3.h include/ncbi/objtseq.h include/ncbi/odlbox.h include/ncbi/panels.h @@ -451,15 +444,16 @@ 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 include/ncbi/taxblast.h include/ncbi/taxext.h 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 @@ -502,6 +496,7 @@ 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 @@ -520,12 +515,9 @@ 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 lib/ncbi/libblast.a @@ -557,16 +549,17 @@ %%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 -%%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html %%PORTDOCS%%%%DOCSDIR%%/blast/fastacmd.html %%PORTDOCS%%%%DOCSDIR%%/blast/filter.html %%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html +%%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html %%PORTDOCS%%%%DOCSDIR%%/blast/impala.html %%PORTDOCS%%%%DOCSDIR%%/blast/index.html %%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html @@ -603,27 +596,32 @@ %%PORTDOCS%%%%DOCSDIR%%/images/seqn20.png %%PORTDOCS%%%%DOCSDIR%%/images/seqn21.png %%PORTDOCS%%%%DOCSDIR%%/images/seqn22.png -%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 -%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1 +%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 +%%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1 +%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1 %%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1 +%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1 +%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1 +%%PORTDOCS%%%%DOCSDIR%%/man/blast.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastall.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1 -%%PORTDOCS%%%%DOCSDIR%%/man/blast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1 %%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1 +%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1 %%PORTDOCS%%%%DOCSDIR%%/man/copymat.1 %%PORTDOCS%%%%DOCSDIR%%/man/ddv.1 %%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1 %%PORTDOCS%%%%DOCSDIR%%/man/entrcmd.1 %%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1 %%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1 -%%PORTDOCS%%%%DOCSDIR%%/man/fastacmd.1 +%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1 +%%PORTDOCS%%%%DOCSDIR%%/man/udv.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 @@ -632,42 +630,37 @@ %%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1 %%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 %%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1 -%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1 %%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1 %%PORTDOCS%%%%DOCSDIR%%/man/impala.1 %%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1 %%PORTDOCS%%%%DOCSDIR%%/man/makemat.1 %%PORTDOCS%%%%DOCSDIR%%/man/makeset.1 %%PORTDOCS%%%%DOCSDIR%%/man/megablast.1 -%%PORTDOCS%%%%DOCSDIR%%/man/Nentrez.1 %%PORTDOCS%%%%DOCSDIR%%/man/netentcf.1 -%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1 %%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1 %%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1 %%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1 -%%PORTDOCS%%%%DOCSDIR%%/man/udv.1 -%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt %%PORTDOCS%%%%DOCSDIR%%/sdk.doc -%%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif %%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.xml %%PORTDOCS%%%%DOCSDIR%%/seq_install/left.GIF %%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-ie.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-netscape.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/main.xslt -%%PORTDOCS%%%%DOCSDIR%%/seq_install/Makefile %%PORTDOCS%%%%DOCSDIR%%/seq_install/ncbi_sequin.css -%%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif %%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 @@ -678,11 +671,11 @@ %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.html %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.xml -%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js +%%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif %%PORTDOCS%%%%DOCSDIR%%/seq_install/spacer10.GIF %%PORTDOCS%%%%DOCSDIR%%/seq_install/template.xml -%%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie3.css %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie.css 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