Date: Thu, 12 Jan 2006 14:50:02 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/91714: [ maintainer update ] update biology/ncbi-toolkit Message-ID: <200601121750.k0CHo2xk091549@pi.iib.unsam.edu.ar> Resent-Message-ID: <200601121800.k0CI0L4a014945@freefall.freebsd.org>
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>Number: 91714 >Category: ports >Synopsis: [ maintainer update ] update biology/ncbi-toolkit >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Thu Jan 12 18:00:16 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p2 FreeBSD 6.0-RELEASE-p2 #0: Thu Jan 12 11:28:24 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: The included patch brings ncbi-toolkit to the version released in December, 2005. This version contains BLAST 2.2.13, and the important changes are summarized below (also available from http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml#20051206) Standalone BLAST 2.2.13 is now available from the BLAST download page. Major changes include: New engine now available in blastall Statistical parameter change Bug fixes New engine available in blastall Blastall now has support for a new version of the BLAST engine that can be enabled by adding "-V F" to the blastall command-line. This option will probably be the default in future versions. There are a few situations where it is very advantageous to use the new engine: Large word-sizes with a BLASTN search. The new engine uses the "stride" idea of AGBLAST and this can lead to a considerable speedup for large wordsizes. For a run of a typical mRNA sequence (u00001) with a word size of 25 the new code runs about twice as fast as the old code. Note that the AG "stride" has been available in megablast since the 2.2.10 release. This enhancement is platform-independent. Searching multiple queries at once. The new engine will search multiple queries by scanning the database once, rather than once for each query. The speedup will depend upon the queries being searched and what part of the time is spent scanning the databases vs. actual compuations (e.g., extensions etc.). Typically this feature is most important if a number of short queries (e.g., mRNA's or EST's) are being searched with blastn or if a tblastn search is performed. This feature is partially supported in the old code with the -B option as well as by megablast. For very large queries. The memory management (especially during the dynamic programming phase) has been improved and this may allow searches with lots of matches or large queries that used to fail to now run to completion. Statistical parameter change Megablast, blastall and bl2seq have until now allowed users to select arbitrary gap existence and extension penalties for a blastn type search. This has been convenient for users but has led to the unfortunate situation that searches with some parameter sets were significantly overestimating the statistical significance of matches. To address this problem the proper statistical parameters for a number of reward/penalty/gap existence/gap extension values have been calculated. The parameters that might cause an issue here are -r (match reward), -q (mismatch penalty), -G (gap existence cost), and -E (gap extension cost). If you do not change these, then nothing will change for you. Please email blast-help@ncbi.nlm.nih.gov with any questions, bug reports, or requests for different parameter sets. Below are listed the supported combinations. Note that above a certain gap existence and extension penalty any value is permitted, as the statistics for ungapped searches can be used. These are marked as "ungapped threshold" below. For match = 1, mismatch = -4 the supported combinations are: G E ----- 1, 2, 0, 2, 2, 1, 1, 1, 2, 2 (ungapped threshold) match = 2, mismatch = -7 the supported combinations are: G E ----- 2, 4, 0, 4, 4, 2, 2, 2, 4, 4 (ungapped threshold) match = 1, mismatch = -3 the supported combinations are: G E ----- 1, 2, 0, 2, 2, 1, 1, 1 2, 2 (ungapped threshold) match = 2, mismatch = -5 the supported combinations are: G E ----- 2, 4, 0, 4, 4, 2, 2, 2, 4, 4 (ungapped threshold) match - 1, mismatch = -2 the supported combinations are: G E ----- 1, 2, 0, 2, 3, 1, 2, 1, 1, 1, 2, 2 (ungapped threshold) match = 2, mismatch = -3 the supported combinations are: G E ----- 4, 4, 2, 4, 0, 4, 3, 3, 6, 2, 5, 2, 4, 2, 2, 2, 6, 4 (ungapped threshold) match = 1, mismatch = -1 the supported combinations are: G E ----- 3, 2, 2, 2, 1, 2, 0, 2, 4, 1, 3, 1, 2, 1, 4, 2 (ungapped threshold) match = 5, mismatch = -4 the supported combinations are: G E ----- 10, 6 8, 6 25, 10 (ungapped threshold) match = 4, mismatch = -5 the supported combinations are: G E ----- 6, 5, 5, 5, 4, 5, 3, 5, 12, 8 (ungapped threshold) Bug fixes A bug has been fixed in formatdb. This bug occurred when the -o option was not used, meaning that the FASTA definition lines of the input file were not parsed, and multiple database volumes were generated. The bug normally did not become apparent to the user until the BLAST run at which point the BLAST binary (e.g., blastall) would produce messages containing "ObjMgrChoice: pointer [0] type [1] not found". >How-To-Repeat: >Fix: --- ncbi-toolkit.diff begins here --- diff -ruN /usr/ports/biology/ncbi-toolkit/Makefile ncbi-toolkit/Makefile --- /usr/ports/biology/ncbi-toolkit/Makefile Mon Oct 17 05:23:08 2005 +++ ncbi-toolkit/Makefile Wed Jan 11 13:28:28 2006 @@ -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 @@ # 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 @@ .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 -ruN /usr/ports/biology/ncbi-toolkit/distinfo ncbi-toolkit/distinfo --- /usr/ports/biology/ncbi-toolkit/distinfo Mon Oct 17 05:23:08 2005 +++ ncbi-toolkit/distinfo Tue Dec 13 10:37:17 2005 @@ -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 -ruN /usr/ports/biology/ncbi-toolkit/files/pkg-message.in ncbi-toolkit/files/pkg-message.in --- /usr/ports/biology/ncbi-toolkit/files/pkg-message.in Wed Dec 31 21:00:00 1969 +++ ncbi-toolkit/files/pkg-message.in Tue Dec 13 10:18:55 2005 @@ -0,0 +1,10 @@ +===================================================================== + +The data files are installed in "%%PREFIX%%/share/ncbi-toolkit". +To use them you need to create a .ncbirc file in your home directory +with the following lines: + +[NCBI] +Data=%%PREFIX%%/share/ncbi-toolkit/ + +===================================================================== diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-message ncbi-toolkit/pkg-message --- /usr/ports/biology/ncbi-toolkit/pkg-message Mon Oct 17 05:23:08 2005 +++ ncbi-toolkit/pkg-message Wed Dec 31 21:00:00 1969 @@ -1,10 +0,0 @@ -===================================================================== - -The data files are installed in "%%PREFIX%%/share/ncbi-toolkit". -To use them you need to create a .ncbirc file in your home directory -with the following lines: - -[NCBI] -Data=%%PREFIX%%/share/ncbi-toolkit/ - -===================================================================== diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-plist ncbi-toolkit/pkg-plist --- /usr/ports/biology/ncbi-toolkit/pkg-plist Mon Oct 17 05:23:11 2005 +++ ncbi-toolkit/pkg-plist Wed Jan 11 09:44:03 2006 @@ -14,8 +14,10 @@ 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/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_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/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/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/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/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/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/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/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 @@ %%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 @@ %%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 @@ %%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 @@ -630,7 +639,6 @@ %%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 @@ -639,10 +647,8 @@ %%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 %%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1 %%PORTDOCS%%%%DOCSDIR%%/man/makemat.1 %%PORTDOCS%%%%DOCSDIR%%/man/makeset.1 @@ -712,6 +718,12 @@ %%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 +756,4 @@ %%PORTDOCS%%@dirrm %%DOCSDIR%%/man %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install %%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%DATADIR%% +@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true --- ncbi-toolkit.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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