Date: Tue, 11 Oct 2005 13:39:27 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/87266: [maintainer update] upgrade biology/ncbi-toolkit to last version Message-ID: <200510111639.j9BGdRLT032797@pi.iib.unsam.edu.ar> Resent-Message-ID: <200510111650.j9BGoE8N023315@freefall.freebsd.org>
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>Number: 87266 >Category: ports >Synopsis: [maintainer update] upgrade biology/ncbi-toolkit to last version >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: Tue Oct 11 16:50:14 GMT 2005 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 4.10-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan@pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386 >Description: No sweeping changes to the port. Added WWW link in pkg-descr, to a page that summarizes changes to the toolkit (a la changelog) Very minor changes in the Makefile (tabs, mostly) >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 Sep 19 05:22:25 2005 +++ ncbi-toolkit/Makefile Wed Oct 5 12:53:16 2005 @@ -7,8 +7,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2004.10.20 -PORTREVISION= 1 +PORTVERSION= 2005.06.05 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -28,7 +27,7 @@ # 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!) +# (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 @@ -41,16 +40,16 @@ X11_EXE= Nentrez Psequin ddv entrez2 netentcf udv # and these are the man pages we have -MAN1= Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \ - asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 copymat.1 ddv.1 \ - debruijn.1 entrcmd.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \ - fmerge.1 formatdb.1 gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 \ - idfetch.1 indexpub.1 makemat.1 makeset.1 netentcf.1 rpsblast.1 \ - tbl2asn.1 udv.1 vecscreen.1 - -MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \ - blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \ - blast.1 seedtop.1 +MAN1= Nentrez.1 Psequin.1 asn2asn.1 asn2ff.1 asn2gb.1 asn2xml.1 asndhuff.1 \ + asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 copymat.1 ddv.1 \ + debruijn.1 entrcmd.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \ + fmerge.1 formatdb.1 gbseqget.1 getfeat.1 getmesh.1 getpub.1 gil2bin.1 \ + idfetch.1 indexpub.1 makemat.1 makeset.1 netentcf.1 rpsblast.1 \ + tbl2asn.1 udv.1 vecscreen.1 + +MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \ + blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \ + blast.1 seedtop.1 # the ncbi-toolkit provides a shell script to drive the build # and we use it diff -ruN /usr/ports/biology/ncbi-toolkit/distinfo ncbi-toolkit/distinfo --- /usr/ports/biology/ncbi-toolkit/distinfo Mon Mar 21 05:23:33 2005 +++ ncbi-toolkit/distinfo Wed Oct 5 11:41:33 2005 @@ -1,2 +1,2 @@ -MD5 (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 3f82bce2a3ce549f055ff989a4b825ed -SIZE (ncbi-toolkit-2004.10.20/ncbi.tar.gz) = 13867811 +MD5 (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 61864b4999390eb69e60734b3b02c149 +SIZE (ncbi-toolkit-2005.06.05/ncbi.tar.gz) = 14458684 diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-descr ncbi-toolkit/pkg-descr --- /usr/ports/biology/ncbi-toolkit/pkg-descr Mon Sep 30 16:23:37 2002 +++ ncbi-toolkit/pkg-descr Wed Oct 5 12:46:49 2005 @@ -17,3 +17,5 @@ applications. -- Tony Maher <tonym@biolateral.com.au> + +WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml diff -ruN /usr/ports/biology/ncbi-toolkit/pkg-message ncbi-toolkit/pkg-message --- /usr/ports/biology/ncbi-toolkit/pkg-message Mon Sep 30 16:23:37 2002 +++ ncbi-toolkit/pkg-message Wed Oct 5 12:35:49 2005 @@ -1,6 +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-plist ncbi-toolkit/pkg-plist --- /usr/ports/biology/ncbi-toolkit/pkg-plist Mon Mar 21 05:23:33 2005 +++ ncbi-toolkit/pkg-plist Wed Oct 5 12:31:58 2005 @@ -39,6 +39,7 @@ bin/udv include/ncbi/connect/connect_export.h 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 @@ -49,6 +50,7 @@ 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_heapmgr.h include/ncbi/connect/ncbi_host_info.h include/ncbi/connect/ncbi_host_infop.h @@ -61,16 +63,20 @@ include/ncbi/connect/ncbi_server_infop.h include/ncbi/connect/ncbi_service.h include/ncbi/connect/ncbi_service_connector.h +include/ncbi/connect/ncbi_service_misc.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_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 @@ -108,6 +114,7 @@ include/ncbi/asnblock.h include/ncbi/asncode.h include/ncbi/asnent2.h +include/ncbi/asnentgene.h include/ncbi/asnfdef.h include/ncbi/asnfeat.h include/ncbi/asngbseq.h @@ -192,8 +199,8 @@ include/ncbi/drawseq.h include/ncbi/dust.h include/ncbi/dvncode.h -include/ncbi/echo_asn.h include/ncbi/edutil.h +include/ncbi/egkludge.h include/ncbi/ent2api.h include/ncbi/entrez.h include/ncbi/entrez2.h @@ -272,8 +279,6 @@ include/ncbi/motif.h include/ncbi/ncbi.h include/ncbi/ncbibs.h -include/ncbi/ncbibuf.h -include/ncbi/ncbicli.h include/ncbi/ncbidraw.h include/ncbi/ncbienv.h include/ncbi/ncbierr.h @@ -293,14 +298,12 @@ include/ncbi/ncbisam.h include/ncbi/ncbisami.h include/ncbi/ncbisgml.h -include/ncbi/ncbisock.h include/ncbi/ncbisort.h include/ncbi/ncbisrti.h include/ncbi/ncbistd.h include/ncbi/ncbistr.h include/ncbi/ncbithr.h include/ncbi/ncbitime.h -include/ncbi/ncbiurl.h include/ncbi/ncbiwin.h include/ncbi/ncbiwww.h include/ncbi/needleman.h @@ -320,6 +323,7 @@ include/ncbi/ni_msg.h include/ncbi/ni_net.h include/ncbi/ni_types.h +include/ncbi/nlm_numerics.h include/ncbi/objacces.h include/ncbi/objalign.h include/ncbi/objalignloc.h @@ -330,7 +334,9 @@ include/ncbi/objcdd.h include/ncbi/objcn3d.h include/ncbi/objcode.h +include/ncbi/objegkludge.h include/ncbi/objent2.h +include/ncbi/objentgene.h include/ncbi/objentr.h include/ncbi/objfdef.h include/ncbi/objfeat.h @@ -385,6 +391,7 @@ include/ncbi/pubdesc.h include/ncbi/puberr.h include/ncbi/qblastapi.h +include/ncbi/re_newton.h include/ncbi/readdb.h include/ncbi/regex.h include/ncbi/rpsutil.h @@ -560,11 +567,14 @@ %%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/web_blast.pl %%PORTDOCS%%%%DOCSDIR%%/blastdb.txt %%PORTDOCS%%%%DOCSDIR%%/blastftp.txt %%PORTDOCS%%%%DOCSDIR%%/dispatcher.html @@ -573,6 +583,7 @@ %%PORTDOCS%%%%DOCSDIR%%/firedialog.gif %%PORTDOCS%%%%DOCSDIR%%/firewall.html %%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh +%%PORTDOCS%%%%DOCSDIR%%/gene2xml.txt %%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css %%PORTDOCS%%%%DOCSDIR%%/images/seqn01.png %%PORTDOCS%%%%DOCSDIR%%/images/seqn02.png --- ncbi-toolkit.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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