mirror of
https://git.FreeBSD.org/ports.git
synced 2024-10-22 20:41:26 +00:00
- Update to 2012.06.20
PR: 176544 Submitted by: Ports Fury
This commit is contained in:
parent
4b7b3683c2
commit
1b607e2b11
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=314129
@ -2,18 +2,20 @@
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# $FreeBSD$
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PORTNAME= ncbi-toolkit
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PORTVERSION= 2009.03.01 # containing BLAST v2.2.19
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PORTREVISION= 1
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PORTVERSION= 2012.06.20 # containing BLAST v2.2.27
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
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MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
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DISTNAME= ncbi
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DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
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MAINTAINER= ports@FreeBSD.org
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COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
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OPTIONS_DEFINE= DOCS
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USE_MOTIF= yes
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CPIO_ARGS= --quiet -pdum -R
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MAKE_JOBS_UNSAFE= yes
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SUB_FILES= pkg-message
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# These are the executables we install.
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@ -28,32 +30,42 @@ SUB_FILES= pkg-message
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# change in the future with the addition of selectable knobs or
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# new slave ports
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TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \
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debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \
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idfetch indexpub makeset tbl2asn vecscreen demo_regexp \
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demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp
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TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
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checksub debruijn demo_regexp demo_regexp_grep dosimple \
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entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
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gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
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vecscreen
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BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \
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fastacmd formatdb formatrpsdb impala makemat megablast \
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rpsblast seedtop taxblast
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X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv
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# and these are the man pages we have
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MAN1= Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \
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asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \
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cdscan.1 checksub.1 copymat.1 ddv.1 \
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debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
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fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \
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idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \
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tbl2asn.1 udv.1 vecscreen.1
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MAN1= Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
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asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
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copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
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fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
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getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
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taxblast.1 tbl2asn.1 udv.1 vecscreen.1
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MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
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blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
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blast.1 seedtop.1 blast.1 rpsblast.1
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MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
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blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
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blast.1 seedtop.1 blast.1 rpsblast.1
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.include <bsd.port.options.mk>
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post-patch:
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@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \
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${WRKSRC}/make/makedis.csh \
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${WRKSRC}/platform/freebsd.ncbi.mk
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@${REINPLACE_CMD} -e \
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's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh
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@${REINPLACE_CMD} -e \
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'/^NCBI_CC/s|=.*|= ${CC}| ; \
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/^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \
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/^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \
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s|-I/usr/X11R6/include||g ; \
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s|-L/usr/X11R6/lib||g ; \
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s|/usr/local|${LOCALBASE}|g ; \
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s|-Wl,-Bstatic|| ; \
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s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk
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# the ncbi-toolkit provides a shell script to drive the build
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# and we use it
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@ -68,36 +80,33 @@ do-install:
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.for blastexe in ${BLAST_EXE}
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin)
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.endfor
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.for toolkitexe in ${TOOLKIT_EXE}
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin)
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.endfor
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.for x11exe in ${X11_EXE}
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(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin)
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.endfor
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@${MKDIR} ${PREFIX}/lib/${DISTNAME}
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(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME})
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@${MKDIR} ${PREFIX}/include/${DISTNAME}
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(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
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${PREFIX}/include/${DISTNAME})
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@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect
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(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME})
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(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}/connect)
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(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
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${PREFIX}/include/${DISTNAME}/connect)
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.for man in ${MAN1}
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(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1)
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(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${MANPREFIX}/man/man1)
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.endfor
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post-install:
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@${MKDIR} ${DATADIR}
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(cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})
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.if !defined(NOPORTDOCS)
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(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${DATADIR})
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.if ${PORT_OPTIONS:MDOCS}
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@${MKDIR} ${DOCSDIR}
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(cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})
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.endif
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.if !defined(BATCH)
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@ ${CAT} ${PKGMESSAGE}
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@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
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(cd ${DOCSDIR} && ${TAR} --unlink -xf -)
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@${FIND} ${DOCSDIR} | ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP}
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@${FIND} ${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
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@${FIND} ${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
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.endif
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@${CAT} ${PKGMESSAGE}
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.include <bsd.port.mk>
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@ -1,2 +1,2 @@
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SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df
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SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732
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SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c
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SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744
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|
11
biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c
Normal file
11
biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c
Normal file
@ -0,0 +1,11 @@
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--- corelib/ncbimisc.c.orig
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+++ corelib/ncbimisc.c
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@@ -1266,7 +1266,7 @@
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if (len < 1) return NULL;
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rsult = (Nlm_CharPtr) MemNew (len + 3);
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- if (rsult == NULL) return;
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+ if (rsult == NULL) return NULL;
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tmp = rsult;
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for (i = 0; /* local [i] != NULL */ i < numitems; i++) {
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@ -8,7 +8,7 @@
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SEQUIN_OPTS =
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LIBCOPY = cp -p
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SRCCOPY = ./ln-if-absent
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@@ -923,17 +924,17 @@
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@@ -934,17 +935,17 @@
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$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
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$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
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$(LIBCOMPADJ) $(LIB2) $(LIB1) \
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@ -17,19 +17,19 @@
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udv : $(OBJUDV)
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$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
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$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
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$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
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$(LIB23) $(LIBCOMPADJ) $(LIB2) \
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- $(LIB1) $(VIBLIBS) $(OTHERLIBS)
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+ $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
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Nentrez : entrez.c $(ULIB31)
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$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
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- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
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+ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
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- $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
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+ $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
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# left this in (Tentrez) for script backwards compatibility
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Tentrez : entrez.c $(ULIB31)
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@@ -1114,7 +1115,7 @@
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@@ -1140,7 +1141,7 @@
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entrez2 : entrez2.c
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$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
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$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
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@ -38,7 +38,7 @@
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$(VIB_POST_LINK) entrez2
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# demo program (spidey)
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@@ -1383,7 +1384,7 @@
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@@ -1421,7 +1422,7 @@
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$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
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$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
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$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
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@ -47,7 +47,7 @@
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$(VIB_POST_LINK) Psequin
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# 'sbtedit' Submission Template Editor
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@@ -1395,7 +1396,7 @@
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@@ -1433,7 +1434,7 @@
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$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
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$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
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$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
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@ -55,4 +55,4 @@
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+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
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$(VIB_POST_LINK) sbtedit
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salogif.o: salogif.c
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# 'streamer' Sequinesque Stream Editor
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|
@ -16,4 +16,4 @@ From the README:
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have found it a useful and stable basis for a number of tools and
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applications.
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WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
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WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
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|
@ -1,87 +1,51 @@
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bin/bl2seq
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bin/blastall
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bin/blastcl3
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bin/blastclust
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bin/blastpgp
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bin/copymat
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bin/fastacmd
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bin/formatdb
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bin/formatrpsdb
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bin/impala
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bin/makemat
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bin/megablast
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bin/rpsblast
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bin/seedtop
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bin/taxblast
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bin/Nentrez
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bin/Psequin
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bin/asn2ff
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bin/asn2gb
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bin/asn2idx
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bin/asn2xml
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bin/asndhuff
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bin/asntool
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bin/bl2seq
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bin/blastall
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bin/blastcl3
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bin/blastclust
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bin/blastpgp
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bin/cdscan
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bin/checksub
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bin/debruijn
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bin/entrcmd
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bin/fa2htgs
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bin/findspl
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bin/getmesh
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bin/getpub
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bin/copymat
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bin/ddv
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bin/gil2bin
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bin/idfetch
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bin/indexpub
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bin/makeset
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bin/tbl2asn
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bin/vecscreen
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bin/debruijn
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bin/demo_regexp
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bin/demo_regexp_grep
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bin/errhdr
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bin/gene2xml
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bin/ncbisort
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bin/seqtest
|
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bin/test_regexp
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bin/Nentrez
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bin/Psequin
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bin/dosimple
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bin/entrcmd
|
||||
bin/entrez2
|
||||
bin/errhdr
|
||||
bin/fa2htgs
|
||||
bin/fastacmd
|
||||
bin/findspl
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bin/formatdb
|
||||
bin/formatrpsdb
|
||||
bin/gene2xml
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||||
bin/getmesh
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||||
bin/getpub
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||||
bin/gil2bin
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||||
bin/idfetch
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||||
bin/impala
|
||||
bin/indexpub
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||||
bin/makemat
|
||||
bin/makeset
|
||||
bin/megablast
|
||||
bin/ncbisort
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||||
bin/rpsblast
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||||
bin/sbtedit
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||||
bin/seedtop
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||||
bin/seqtest
|
||||
bin/taxblast
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||||
bin/tbl2asn
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||||
bin/udv
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||||
include/ncbi/connect/connect_export.h
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||||
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
|
||||
%%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%%
|
||||
@dirrm lib/ncbi
|
||||
@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
|
||||
%%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
|
||||
%%PORTDOCS%%@dirrm %%DOCSDIR%%
|
||||
@dirrmtry %%DATADIR%%
|
||||
|
Loading…
Reference in New Issue
Block a user