diff options
Diffstat (limited to 'biology/ncbi-toolkit')
| -rw-r--r-- | biology/ncbi-toolkit/Makefile | 84 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/distinfo | 5 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c | 11 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-make-makenet.unx | 58 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-descr | 2 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-plist | 102 |
6 files changed, 87 insertions, 175 deletions
diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index 1dd59de66e03..b3c92f114493 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -2,56 +2,33 @@ # $FreeBSD$ PORTNAME= ncbi-toolkit -PORTVERSION= 2012.06.20 # containing BLAST v2.2.27 -PORTREVISION= 1 +DISTVERSION= 2017.01.06 # containing BLAST v2.2.27 (? is this true) CATEGORIES= biology 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 +MAINTAINER= yuri@FreeBSD.org COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support -LIB_DEPENDS= libpng.so:graphics/png - -USES= iconv motif -MAKE_JOBS_UNSAFE= yes +LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ + libgmp.so:math/gmp \ + libgnutls.so:security/gnutls \ + libhogweed.so:security/nettle \ + libidn2.so:dns/libidn2 \ + libnettle.so:security/nettle \ + libp11-kit.so:security/p11-kit \ + libpng.so:graphics/png \ + libtasn1.so:security/libtasn1 \ + libtspi.so:security/trousers \ + libunistring.so:devel/libunistring \ + libXp.so:x11/libXp + +USES= gettext-runtime iconv jpeg motif +USE_XORG= x11 xau xext xft xmu xrender xt SUB_FILES= pkg-message -# These are the executables we install. -# -# 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 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 -MAN_FILES= 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 - -MAN_LINKS= bl2seq blastall blastcl3 blastpgp impala megablast \ - seedtop rpsblast - OPTIONS_DEFINE= DOCS post-patch: @@ -73,30 +50,25 @@ post-patch: # and we use it do-build: - cd ${WRKDIR}; ./${DISTNAME}/make/makedis.csh + @cd ${WRKDIR} && ./${DISTNAME}/make/makedis.csh # the ncbi-toolkit does not provide an install target # we thus roll our own do-install: - (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${BLAST_EXE} \ - ${TOOLKIT_EXE} ${X11_EXE} ${STAGEDIR}${PREFIX}/bin) + cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin @${MKDIR} ${STAGEDIR}${PREFIX}/lib/${DISTNAME} - (cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \ - ${STAGEDIR}${PREFIX}/lib/${DISTNAME}) + cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \ + ${STAGEDIR}${PREFIX}/lib/${DISTNAME} @${MKDIR} ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect - (cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \ - ${STAGEDIR}${PREFIX}/include/${DISTNAME}) - (cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \ - ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect) - (cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${MAN_FILES} \ - ${STAGEDIR}${MANPREFIX}/man/man1) -.for man in ${MAN_LINKS} - ${LN} -s ${MANPREFIX}/man/man1/blast.1.gz \ - ${STAGEDIR}${PREFIX}/man/man1/${man}.1.gz -.endfor + cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \ + ${STAGEDIR}${PREFIX}/include/${DISTNAME} + cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \ + ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect + cd ${WRKSRC}/doc/man && ${INSTALL_MAN} * \ + ${STAGEDIR}${MANPREFIX}/man/man1 @${MKDIR} ${STAGEDIR}${DATADIR} - (cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}) + cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR} do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo index 8b767a5e8fd1..25a7e4952002 100644 --- a/biology/ncbi-toolkit/distinfo +++ b/biology/ncbi-toolkit/distinfo @@ -1,2 +1,3 @@ -SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c -SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744 +TIMESTAMP = 1538934016 +SHA256 (ncbi-toolkit-2017.01.06/ncbi.tar.gz) = 4b88aaad8f953b1b50bc7d06f3a5920f0d589d2c9a26c709199f8347905f5867 +SIZE (ncbi-toolkit-2017.01.06/ncbi.tar.gz) = 155731358 diff --git a/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c b/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c deleted file mode 100644 index 095c6231ba55..000000000000 --- a/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c +++ /dev/null @@ -1,11 +0,0 @@ ---- 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 deleted file mode 100644 index 2e51654e29e1..000000000000 --- a/biology/ncbi-toolkit/files/patch-make-makenet.unx +++ /dev/null @@ -1,58 +0,0 @@ ---- make/makenet.unx.orig 2008-12-11 00:23:29.000000000 +0300 -+++ make/makenet.unx 2011-04-14 00:26:38.440426134 +0400 -@@ -67,6 +67,7 @@ - VIB = - VIBLIBS= -lXm -lXmu -lXt -lX11 - VIBLIBS= -+USERLIBS = -lXft -lpng -ljpeg %%ICONV_LIB%% - SEQUIN_OPTS = - LIBCOPY = cp -p - SRCCOPY = ./ln-if-absent -@@ -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) \ -- $(VIBLIBS) $(OTHERLIBS) -+ $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) - - udv : $(OBJUDV) - $(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \ - $(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) - - # left this in (Tentrez) for script backwards compatibility - Tentrez : entrez.c $(ULIB31) -@@ -1140,7 +1141,7 @@ - entrez2 : entrez2.c - $(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \ - $(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \ -- $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS) -+ $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) - $(VIB_POST_LINK) entrez2 - - # demo program (spidey) -@@ -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) \ -- $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) -+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) - $(VIB_POST_LINK) Psequin - - # 'sbtedit' Submission Template Editor -@@ -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) \ -- $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) -+ $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS) - $(VIB_POST_LINK) sbtedit - - # 'streamer' Sequinesque Stream Editor diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr index 35331ba63d4d..2c44aef32154 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/IEB/ToolBox/MainPage/index.html +WWW: https://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 efd3cb71ee07..24f92e502b77 100644 --- a/biology/ncbi-toolkit/pkg-plist +++ b/biology/ncbi-toolkit/pkg-plist @@ -6,14 +6,9 @@ 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 @@ -23,27 +18,22 @@ bin/entrcmd bin/entrez2 bin/errhdr bin/fa2htgs -bin/fastacmd bin/findspl -bin/formatdb -bin/formatrpsdb bin/gene2xml bin/getmesh bin/getpub bin/gil2bin bin/idfetch -bin/impala bin/indexpub -bin/makemat bin/makeset -bin/megablast bin/ncbisort -bin/rpsblast bin/sbtedit -bin/seedtop bin/seqtest -bin/taxblast bin/tbl2asn +bin/test_regexp +bin/testcore +bin/testobj +bin/testval bin/udv bin/vecscreen include/ncbi/FSpCompat.h @@ -186,7 +176,10 @@ 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_ipv6.h include/ncbi/connect/ncbi_lb.h +include/ncbi/connect/ncbi_lbos.h +include/ncbi/connect/ncbi_lbosp.h include/ncbi/connect/ncbi_lbsmd.h include/ncbi/connect/ncbi_local.h include/ncbi/connect/ncbi_memory_connector.h @@ -564,6 +557,7 @@ include/ncbi/xmlblast.h lib/ncbi/libblast.a lib/ncbi/libblastapi.a lib/ncbi/libblastcompadj.a +lib/ncbi/libconnssl.a lib/ncbi/libddvlib.a lib/ncbi/libncbi.a lib/ncbi/libncbiCacc.a @@ -586,41 +580,46 @@ lib/ncbi/libvibgif.a lib/ncbi/libvibnet.a lib/ncbi/libvibrant.a man/man1/Psequin.1.gz +man/man1/asn2all.1.gz +man/man1/asn2asn.1.gz man/man1/asn2ff.1.gz +man/man1/asn2fsa.1.gz +man/man1/asn2gb.1.gz man/man1/asn2idx.1.gz man/man1/asn2xml.1.gz man/man1/asndhuff.1.gz +man/man1/asndisc.1.gz +man/man1/asnmacro.1.gz man/man1/asntool.1.gz -man/man1/bl2seq.1.gz -man/man1/blast.1.gz -man/man1/blastall.1.gz +man/man1/asnval.1.gz man/man1/blastcl3.1.gz -man/man1/blastclust.1.gz -man/man1/blastpgp.1.gz man/man1/cdscan.1.gz man/man1/checksub.1.gz -man/man1/copymat.1.gz +man/man1/cleanasn.1.gz man/man1/ddv.1.gz man/man1/debruijn.1.gz man/man1/entrez2.1.gz man/man1/errhdr.1.gz man/man1/fa2htgs.1.gz -man/man1/fastacmd.1.gz man/man1/findspl.1.gz -man/man1/formatdb.1.gz -man/man1/formatrpsdb.1.gz +man/man1/fmerge.1.gz +man/man1/gbseqget.1.gz +man/man1/gene2xml.1.gz man/man1/getmesh.1.gz man/man1/getpub.1.gz man/man1/gil2bin.1.gz man/man1/idfetch.1.gz -man/man1/impala.1.gz man/man1/indexpub.1.gz -man/man1/makemat.1.gz -man/man1/megablast.1.gz -man/man1/rpsblast.1.gz -man/man1/seedtop.1.gz -man/man1/taxblast.1.gz +man/man1/insdseqget.1.gz +man/man1/makeset.1.gz +man/man1/nps2gps.1.gz +man/man1/sbtedit.1.gz +man/man1/sortbyquote.1.gz +man/man1/spidey.1.gz +man/man1/subfuse.1.gz man/man1/tbl2asn.1.gz +man/man1/trna2sap.1.gz +man/man1/trna2tbl.1.gz man/man1/udv.1.gz man/man1/vecscreen.1.gz %%PORTDOCS%%%%DOCSDIR%%/FAQ.txt @@ -629,26 +628,8 @@ man/man1/vecscreen.1.gz %%PORTDOCS%%%%DOCSDIR%%/access.txt %%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt %%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt -%%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/fastacmd.html %%PORTDOCS%%%%DOCSDIR%%/blast/filter.html -%%PORTDOCS%%%%DOCSDIR%%/blast/formatdb.html -%%PORTDOCS%%%%DOCSDIR%%/blast/formatrpsdb.html -%%PORTDOCS%%%%DOCSDIR%%/blast/history.html -%%PORTDOCS%%%%DOCSDIR%%/blast/impala.html -%%PORTDOCS%%%%DOCSDIR%%/blast/index.html -%%PORTDOCS%%%%DOCSDIR%%/blast/megablast.html %%PORTDOCS%%%%DOCSDIR%%/blast/netblast.html -%%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html -%%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf -%%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html -%%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc @@ -761,12 +742,36 @@ man/man1/vecscreen.1.gz %%DATADIR%%/LSURef_93.fasta.nhr %%DATADIR%%/LSURef_93.fasta.nin %%DATADIR%%/LSURef_93.fasta.nsq +%%DATADIR%%/LSU_chloro_rRNA.nhr +%%DATADIR%%/LSU_chloro_rRNA.nin +%%DATADIR%%/LSU_chloro_rRNA.nsq +%%DATADIR%%/LSU_mito_rRNA.nhr +%%DATADIR%%/LSU_mito_rRNA.nin +%%DATADIR%%/LSU_mito_rRNA.nsq +%%DATADIR%%/LSU_nomito-nochloro-noplastid.nhr +%%DATADIR%%/LSU_nomito-nochloro-noplastid.nin +%%DATADIR%%/LSU_nomito-nochloro-noplastid.nsq +%%DATADIR%%/LSU_plastid.nhr +%%DATADIR%%/LSU_plastid.nin +%%DATADIR%%/LSU_plastid.nsq %%DATADIR%%/PAM250 %%DATADIR%%/PAM30 %%DATADIR%%/PAM70 +%%DATADIR%%/SSU-mito-rRNA.nhr +%%DATADIR%%/SSU-mito-rRNA.nin +%%DATADIR%%/SSU-mito-rRNA.nsq %%DATADIR%%/SSURef_93.fasta.nhr %%DATADIR%%/SSURef_93.fasta.nin %%DATADIR%%/SSURef_93.fasta.nsq +%%DATADIR%%/SSU_chloro_rRNA.nhr +%%DATADIR%%/SSU_chloro_rRNA.nin +%%DATADIR%%/SSU_chloro_rRNA.nsq +%%DATADIR%%/SSU_nomito_nochloro_noplastid.nhr +%%DATADIR%%/SSU_nomito_nochloro_noplastid.nin +%%DATADIR%%/SSU_nomito_nochloro_noplastid.nsq +%%DATADIR%%/SSU_plast_rRNA.nhr +%%DATADIR%%/SSU_plast_rRNA.nin +%%DATADIR%%/SSU_plast_rRNA.nsq %%DATADIR%%/UniVec.nhr %%DATADIR%%/UniVec.nin %%DATADIR%%/UniVec.nsq @@ -775,6 +780,9 @@ man/man1/vecscreen.1.gz %%DATADIR%%/UniVec_Core.nsq %%DATADIR%%/asn2ff.prt %%DATADIR%%/autofix.prt +%%DATADIR%%/bacteria-archea16SrRNA.nhr +%%DATADIR%%/bacteria-archea16SrRNA.nin +%%DATADIR%%/bacteria-archea16SrRNA.nsq %%DATADIR%%/blast.prt %%DATADIR%%/bstdt.prt %%DATADIR%%/bstdt.val |