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Update to 2001.12.20

Browse Source 
PR:		35203
Submitted by:	maintainer
This commit is contained in:
Patrick Li 2002-02-22 07:57:07 +00:00
parent 826f36f5dc
commit 672a625d5d
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=55075
6 changed files with 88 additions and 18 deletions
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23
biology/ncbi-toolkit/Makefile
View File

@ -6,8 +6,7 @@
#
PORTNAME= ncbi-toolkit
PORTVERSION= 2001.04.03
PORTREVISION= 1
PORTVERSION= 2001.12.20
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME= ncbi
@ -21,11 +20,6 @@ USE_MOTIF= yes
#
DUMMYMAKE= Makefile
#
# out of it for the post-install when we put in system startup file.
#
PLATFORMDIR= ${WRKSRC}/platform
BUILDSCRIPT= ${WRKSRC}/make/makedis.csh
@ -33,11 +27,9 @@ DOCDIR= ${PREFIX}/share/doc/${PORTNAME}
CPIO= cpio --quiet -pdum -R
#
# Thus ends the definitions
# Thus ends the definitions.
#
#
# We need a dummy top level Makefile as NCBI has scripts that need to
# Now we need a dummy top level Makefile as NCBI has scripts that need to
# run from point above ncbi hierachy.
#
@ -47,10 +39,15 @@ pre-configure:
@${PERL} -pi.orig -e 's#NetBSD#FreeBSD#;' -e 's#netbsd#freebsd#' ${BUILDSCRIPT}
post-install:
@${MKDIR} ${DATADIR}
@for file in ${WRKSRC}/data/*; do \
${INSTALL_DATA} $$file ${DATADIR}; \
done
.if !defined(NOPORTDOCS)
@ ${MKDIR} ${DOCDIR}
@ cd ${WRKSRC}/doc && find * | \
@${MKDIR} ${DOCDIR}
@cd ${WRKSRC}/doc && find * | \
${CPIO} ${SHAREOWN}:${SHAREGRP} ${DOCDIR}
.endif
@${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE}
.include <bsd.port.mk>

2
biology/ncbi-toolkit/distinfo
View File

@ -1 +1 @@
MD5 (ncbi.tar.gz) = 7bbfecf047f4e43c4e7bc292865c3485
MD5 (ncbi.tar.gz) = 8038afb3f5502b3b8ade4f221eebe46e

4
biology/ncbi-toolkit/files/freebsd.ncbi.mk
View File

@ -25,3 +25,7 @@ NCBI_RANLIB = ranlib
NCBI_MT_OTHERLIBS =
NCBI_THREAD_OBJ = ncbithr.o
NETENTREZVERSION = 2.02c2ASN1SPEC6
NCBI_LBSM_SRC = ncbi_service_lbsmd_stub.c
NCBI_LBSM_OBJ = ncbi_service_lbsmd_stub.o

2
biology/ncbi-toolkit/files/patch-aa
View File

@ -6,7 +6,7 @@
$(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl
+
+EXE= Nentrez Psequin \
+ asn2fast asn2ff asndhuff asntool \
+ asn2fast asn2ff asn2xml asndhuff asntool \
+ bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \
+ cdscan checksub copymat \
+ ddv dosimple \

8
biology/ncbi-toolkit/pkg-message Normal file
View File

@ -0,0 +1,8 @@
The data files are installed in "%%PREFIX%%/share/ncbi-tookit".
To use them you need to create a .ncbirc file in your home directory
with the following lines:
[NCBI]
Data=%%PREFIX%%/share/ncbi-toolkit/

67
biology/ncbi-toolkit/pkg-plist
View File

@ -44,6 +44,7 @@ bin/Nentrez
bin/Psequin
bin/asn2fast
bin/asn2ff
bin/asn2xml
bin/asndhuff
bin/asntool
bin/bl2seq
@ -116,11 +117,10 @@ include/ncbi/connect/ncbi_core.h
include/ncbi/connect/ncbi_file_connector.h
include/ncbi/connect/ncbi_heapmgr.h
include/ncbi/connect/ncbi_http_connector.h
include/ncbi/connect/ncbi_lbsm.h
include/ncbi/connect/ncbi_lbsm_ipc.h
include/ncbi/connect/ncbi_priv.h
include/ncbi/connect/ncbi_sendmail.h
include/ncbi/connect/ncbi_server_info.h
include/ncbi/connect/ncbi_server_infop.h
include/ncbi/connect/ncbi_service.h
include/ncbi/connect/ncbi_service_connector.h
include/ncbi/connect/ncbi_servicep.h
@ -128,6 +128,7 @@ include/ncbi/connect/ncbi_servicep_dispd.h
include/ncbi/connect/ncbi_servicep_lbsmd.h
include/ncbi/connect/ncbi_socket.h
include/ncbi/connect/ncbi_socket_connector.h
include/ncbi/connect/ncbi_types.h
include/ncbi/connect/ncbi_util.h
include/ncbi/PubStructAsn.h
include/ncbi/a2ferr.h
@ -141,7 +142,10 @@ include/ncbi/actutils.h
include/ncbi/algorend.h
include/ncbi/alignloc.h
include/ncbi/alignmgr.h
include/ncbi/alignmgr2.h
include/ncbi/alignval.h
include/ncbi/aliparse.h
include/ncbi/aliread.h
include/ncbi/all.h
include/ncbi/allpub.h
include/ncbi/apparam.h
@ -151,6 +155,9 @@ include/ncbi/asn2ff6.h
include/ncbi/asn2ffg.h
include/ncbi/asn2ffp.h
include/ncbi/asn2gnbk.h
include/ncbi/asn2gnbp.h
include/ncbi/asn2graphic.h
include/ncbi/asn2graphicp.h
include/ncbi/asnacces.h
include/ncbi/blast.h
include/ncbi/asnalign.h
@ -202,6 +209,7 @@ include/ncbi/cdnewlib.h
include/ncbi/cdrgn.h
include/ncbi/cdrom.h
include/ncbi/cdromlib.h
include/ncbi/cn3d.h
include/ncbi/cn3dentr.h
include/ncbi/cn3dmain.h
include/ncbi/cn3dmesh.h
@ -237,6 +245,7 @@ include/ncbi/echo_asn.h
include/ncbi/edutil.h
include/ncbi/ent2api.h
include/ncbi/entrez.h
include/ncbi/entrez2.h
include/ncbi/errdefn.h
include/ncbi/explore.h
include/ncbi/fastadl.h
@ -265,6 +274,9 @@ include/ncbi/id1map.h
include/ncbi/image.h
include/ncbi/imagelst.h
include/ncbi/import.h
include/ncbi/ingenext.h
include/ncbi/ingengraph.h
include/ncbi/ingenwin.h
include/ncbi/jsavlt.h
include/ncbi/jzcoll.h
include/ncbi/jzmisc.h
@ -275,6 +287,7 @@ include/ncbi/list.h
include/ncbi/lnfac.h
include/ncbi/lookup.h
include/ncbi/lsqfetch.h
include/ncbi/mapcn3d.h
include/ncbi/mapgene.h
include/ncbi/mapmime.h
include/ncbi/mapmla.h
@ -285,7 +298,6 @@ include/ncbi/maputil.h
include/ncbi/matrix.h
include/ncbi/mbalign.h
include/ncbi/mblast.h
include/ncbi/mbutils.h
include/ncbi/mconsist.h
include/ncbi/mdrcherr.h
include/ncbi/medarch.h
@ -303,6 +315,7 @@ include/ncbi/mmdbapi3.h
include/ncbi/mmdbapi4.h
include/ncbi/mmdbdata.h
include/ncbi/mmdblocl.h
include/ncbi/motif.h
include/ncbi/ncbi.h
include/ncbi/ncbibs.h
include/ncbi/ncbibuf.h
@ -361,6 +374,7 @@ include/ncbi/objbibli.h
include/ncbi/objblock.h
include/ncbi/objblst3.h
include/ncbi/objcdd.h
include/ncbi/objcn3d.h
include/ncbi/objcode.h
include/ncbi/objent2.h
include/ncbi/objentr.h
@ -450,6 +464,7 @@ include/ncbi/shim3d.h
include/ncbi/simple.h
include/ncbi/simutil.h
include/ncbi/spell.h
include/ncbi/spidey.h
include/ncbi/splutil.h
include/ncbi/sqnutils.h
include/ncbi/strimprt.h
@ -537,9 +552,55 @@ include/ncbi/wrpsb.h
include/ncbi/wrpsbtool.h
include/ncbi/wwwblast.h
include/ncbi/xmlblast.h
share/ncbi-toolkit/BLOSUM45
share/ncbi-toolkit/BLOSUM62
share/ncbi-toolkit/BLOSUM80
share/ncbi-toolkit/ContactPotential
share/ncbi-toolkit/KSat.flt
share/ncbi-toolkit/KSchoth.flt
share/ncbi-toolkit/KSesigc.mat
share/ncbi-toolkit/KSesigl.mat
share/ncbi-toolkit/KSgc.flt
share/ncbi-toolkit/KShopp.flt
share/ncbi-toolkit/KSkyte.flt
share/ncbi-toolkit/KSmtidk.mat
share/ncbi-toolkit/KSmtk.mat
share/ncbi-toolkit/KSnsigc.mat
share/ncbi-toolkit/KSnsigl.mat
share/ncbi-toolkit/KSpcc.mat
share/ncbi-toolkit/KSpsigc.mat
share/ncbi-toolkit/KSpsigl.mat
share/ncbi-toolkit/KSpur.flt
share/ncbi-toolkit/KSpyr.flt
share/ncbi-toolkit/PAM30
share/ncbi-toolkit/PAM70
share/ncbi-toolkit/asn2ff.prt
share/ncbi-toolkit/blast.prt
share/ncbi-toolkit/bstdt.prt
share/ncbi-toolkit/bstdt.val
share/ncbi-toolkit/featdef.prt
share/ncbi-toolkit/featdef.val
share/ncbi-toolkit/gc.prt
share/ncbi-toolkit/gc.val
share/ncbi-toolkit/humrep.fsa
share/ncbi-toolkit/lineages.txt
share/ncbi-toolkit/makerpt.prt
share/ncbi-toolkit/ncbiendo.dat
share/ncbi-toolkit/ncbipnam.dat
share/ncbi-toolkit/ncbipros.dat
share/ncbi-toolkit/ncbiren.dat
share/ncbi-toolkit/ncbirnam.dat
share/ncbi-toolkit/objprt.prt
share/ncbi-toolkit/pubkey.enc
share/ncbi-toolkit/seqcode.prt
share/ncbi-toolkit/seqcode.val
share/ncbi-toolkit/sequin.hlp
share/ncbi-toolkit/sgmlbb.ent
share/ncbi-toolkit/taxlist.txt
@dirrm include/ncbi/connect
@dirrm include/ncbi
@dirrm lib/ncbi
@dirrm share/ncbi-toolkit
%%PORTDOCS%%@dirrm share/doc/ncbi-toolkit/images
%%PORTDOCS%%@dirrm share/doc/ncbi-toolkit/fa2htgs
%%PORTDOCS%%@dirrm share/doc/ncbi-toolkit