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- Update to 2005.12.06

Browse source 
PR:		ports/91714
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
This commit is contained in:
Pav Lucistnik 2006-01-14 19:34:43 +00:00
parent 54fa0f2a38
commit 5825fa4ce6
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=153494
4 changed files with 60 additions and 44 deletions
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10
biology/ncbi-toolkit/Makefile
View file

@ -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

5
biology/ncbi-toolkit/distinfo
View file

@ -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

0
biology/ncbi-toolkit/pkg-message → biology/ncbi-toolkit/files/pkg-message.in
View file

89
biology/ncbi-toolkit/pkg-plist
View file

@ -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