diff options
| -rw-r--r-- | biology/ncbi-toolkit/Makefile | 10 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/distinfo | 5 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/pkg-message.in (renamed from biology/ncbi-toolkit/pkg-message) | 0 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/pkg-plist | 89 |
4 files changed, 60 insertions, 44 deletions
diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index e9e5946f14d4..b1d3183c1524 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -7,7 +7,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2005.06.05 +PORTVERSION= 2005.12.06 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -32,12 +32,12 @@ PKGMESSAGE= ${WRKDIR}/pkg-message # 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 \ +TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool 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 +X11_EXE= Nentrez Psequin ddv entrez2 netentcf sbtedit udv # and these are the man pages we have MAN1= Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \ @@ -93,7 +93,7 @@ post-install: .endif .if !defined(BATCH) - @ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${.CURDIR}/pkg-message > ${PKGMESSAGE} + @ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${FILESDIR}/pkg-message.in > ${PKGMESSAGE} @ ${CAT} ${PKGMESSAGE} .endif diff --git a/biology/ncbi-toolkit/distinfo b/biology/ncbi-toolkit/distinfo index d9f8d695ff8f..82242ab79d44 100644 --- a/biology/ncbi-toolkit/distinfo +++ b/biology/ncbi-toolkit/distinfo @@ -1,2 +1,3 @@ -MD5 (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 61864b4999390eb69e60734b3b02c149 -SIZE (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 14458684 +MD5 (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 50a83a509b67fd8f317b0da42703de1d +SHA256 (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 0b409557d6601b8703328cd1ae997985677416e9ad9375e57b298113ecaaeeda +SIZE (ncbi-toolkit-2005.12.06/ncbi.tar.gz) = 14693833 diff --git a/biology/ncbi-toolkit/pkg-message b/biology/ncbi-toolkit/files/pkg-message.in index 97eed5af5f33..97eed5af5f33 100644 --- a/biology/ncbi-toolkit/pkg-message +++ b/biology/ncbi-toolkit/files/pkg-message.in diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist index f658dffb0a95..65243b4295eb 100644 --- a/biology/ncbi-toolkit/pkg-plist +++ b/biology/ncbi-toolkit/pkg-plist @@ -14,8 +14,10 @@ bin/rpsblast bin/seedtop bin/asn2ff bin/asn2gb +bin/asn2idx bin/asn2xml bin/asndhuff +bin/asntool bin/checksub bin/debruijn bin/entrcmd @@ -36,6 +38,7 @@ bin/Nentrez bin/Psequin bin/entrez2 bin/netentcf +bin/sbtedit bin/udv include/ncbi/connect/connect_export.h include/ncbi/connect/ncbi_ansi_ext.h @@ -72,11 +75,9 @@ include/ncbi/connect/ncbi_types.h include/ncbi/connect/ncbi_util.h include/ncbi/FSpCompat.h include/ncbi/FullPath.h -include/ncbi/Mode_condition.h include/ncbi/MoreCarbonAccessors.h include/ncbi/MoreFilesExtras.h include/ncbi/MoreFilesX.h -include/ncbi/NRdefs.h include/ncbi/Optimization.h include/ncbi/OptimizationEnd.h include/ncbi/PubStructAsn.h @@ -180,6 +181,10 @@ include/ncbi/cn3dsave.h include/ncbi/cn3dshim.h include/ncbi/cn3dstyl.h include/ncbi/cn3dxprt.h +include/ncbi/compo_heap.h +include/ncbi/compo_mode_condition.h +include/ncbi/composition_adjustment.h +include/ncbi/composition_constants.h include/ncbi/corematx.h include/ncbi/db_list.h include/ncbi/ddvclick.h @@ -257,6 +262,7 @@ include/ncbi/mapproj.h include/ncbi/mappubme.h include/ncbi/maputil.h include/ncbi/matrix.h +include/ncbi/matrix_frequency_data.h include/ncbi/mbalign.h include/ncbi/mblast.h include/ncbi/mconsist.h @@ -313,17 +319,13 @@ include/ncbi/netentr.h include/ncbi/netlib.h include/ncbi/netpriv.h include/ncbi/netscape.h -include/ncbi/ni_asn.h include/ncbi/ni_defin.h -include/ncbi/ni_encr.h include/ncbi/ni_error.h include/ncbi/ni_lib.h include/ncbi/ni_lib_.h -include/ncbi/ni_list.h -include/ncbi/ni_msg.h include/ncbi/ni_net.h include/ncbi/ni_types.h -include/ncbi/nlm_numerics.h +include/ncbi/nlm_linear_algebra.h include/ncbi/objacces.h include/ncbi/objalign.h include/ncbi/objalignloc.h @@ -369,6 +371,7 @@ include/ncbi/objtax1.h include/ncbi/objtax3.h include/ncbi/objtseq.h include/ncbi/odlbox.h +include/ncbi/optimize_target_freq.h include/ncbi/panels.h include/ncbi/parsegb.h include/ncbi/pcre.h @@ -391,8 +394,8 @@ include/ncbi/prunebsc.h include/ncbi/pubdesc.h include/ncbi/puberr.h include/ncbi/qblastapi.h -include/ncbi/re_newton.h include/ncbi/readdb.h +include/ncbi/redo_alignment.h include/ncbi/regex.h include/ncbi/rpsutil.h include/ncbi/saldist.h @@ -437,6 +440,7 @@ include/ncbi/sequtil.h include/ncbi/shim3d.h include/ncbi/simple.h include/ncbi/simutil.h +include/ncbi/smith_waterman.h include/ncbi/spell.h include/ncbi/spellapi.h include/ncbi/spidey.h @@ -529,6 +533,7 @@ include/ncbi/wwwblast.h include/ncbi/xmlblast.h lib/ncbi/libblast.a lib/ncbi/libblastapi.a +lib/ncbi/libblastcompadj.a lib/ncbi/libddvlib.a lib/ncbi/libncbi.a lib/ncbi/libncbiCacc.a @@ -574,9 +579,9 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/blast/netblast.html %%PORTDOCS%%%%DOCSDIR%%/blast/rpsblast.html %%PORTDOCS%%%%DOCSDIR%%/blast/scoring.pdf +%%PORTDOCS%%%%DOCSDIR%%/blast/seedtop.html +%%PORTDOCS%%%%DOCSDIR%%/blast/update_blastdb.pl %%PORTDOCS%%%%DOCSDIR%%/blast/web_blast.pl -%%PORTDOCS%%%%DOCSDIR%%/blastdb.txt -%%PORTDOCS%%%%DOCSDIR%%/blastftp.txt %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/README %%PORTDOCS%%%%DOCSDIR%%/fa2htgs/updateHtgsDoc @@ -584,34 +589,37 @@ 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 +%%PORTDOCS%%%%DOCSDIR%%/images/cds_edit.png +%%PORTDOCS%%%%DOCSDIR%%/images/contact.png +%%PORTDOCS%%%%DOCSDIR%%/images/desktop.png +%%PORTDOCS%%%%DOCSDIR%%/images/format.png +%%PORTDOCS%%%%DOCSDIR%%/images/genbank.png +%%PORTDOCS%%%%DOCSDIR%%/images/graphic.png +%%PORTDOCS%%%%DOCSDIR%%/images/loc_page.png %%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css -%%PORTDOCS%%%%DOCSDIR%%/images/seqn01.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn02.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn03.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn04.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn05.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn06.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn07.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn08.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn09.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn10.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn11.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn12.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn13.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn14.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn15.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn16.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn17.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn18.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn19.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn20.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn21.png -%%PORTDOCS%%%%DOCSDIR%%/images/seqn22.png -%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1 +%%PORTDOCS%%%%DOCSDIR%%/images/net_cfg.png +%%PORTDOCS%%%%DOCSDIR%%/images/nucaln.png +%%PORTDOCS%%%%DOCSDIR%%/images/nucset.png +%%PORTDOCS%%%%DOCSDIR%%/images/nucsing1.png +%%PORTDOCS%%%%DOCSDIR%%/images/nucsing2.png +%%PORTDOCS%%%%DOCSDIR%%/images/organism.png +%%PORTDOCS%%%%DOCSDIR%%/images/props_pg.png +%%PORTDOCS%%%%DOCSDIR%%/images/protein1.png +%%PORTDOCS%%%%DOCSDIR%%/images/protein2.png +%%PORTDOCS%%%%DOCSDIR%%/images/sequence.png +%%PORTDOCS%%%%DOCSDIR%%/images/submit.png +%%PORTDOCS%%%%DOCSDIR%%/images/update.png +%%PORTDOCS%%%%DOCSDIR%%/images/validate.png +%%PORTDOCS%%%%DOCSDIR%%/images/welcome.png +%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.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 @@ -620,6 +628,7 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/man/blast.1 %%PORTDOCS%%%%DOCSDIR%%/man/blastall.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 @@ -630,16 +639,15 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1 %%PORTDOCS%%%%DOCSDIR%%/man/errhdr.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 +%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 %%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1 %%PORTDOCS%%%%DOCSDIR%%/man/getfeat.1 %%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1 -%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1 %%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1 %%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1 %%PORTDOCS%%%%DOCSDIR%%/man/impala.1 @@ -651,6 +659,7 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1 %%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1 %%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1 +%%PORTDOCS%%%%DOCSDIR%%/man/udv.1 %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt %%PORTDOCS%%%%DOCSDIR%%/sdk.doc %%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css @@ -712,6 +721,12 @@ lib/ncbi/libvibrant.a %%DATADIR%%/KSpyr.flt %%DATADIR%%/PAM30 %%DATADIR%%/PAM70 +%%DATADIR%%/UniVec.nhr +%%DATADIR%%/UniVec.nin +%%DATADIR%%/UniVec.nsq +%%DATADIR%%/UniVec_Core.nhr +%%DATADIR%%/UniVec_Core.nin +%%DATADIR%%/UniVec_Core.nsq %%DATADIR%%/asn2ff.prt %%DATADIR%%/blast.prt %%DATADIR%%/bstdt.prt @@ -744,4 +759,4 @@ lib/ncbi/libvibrant.a %%PORTDOCS%%@dirrm %%DOCSDIR%%/man %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install %%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%DATADIR%% +@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true |