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- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1

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- Update the EMBASSY package EMNU from 1.0.2 to 1.0.3
- Merged the four pkg-plist* files into one

PR: 24717
Submitted by: MAINTAINER
This commit is contained in:
Kevin Lo 2001-01-29 15:48:01 +00:00
parent d9d18678eb
commit f34ef8cc9c
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=37757
10 changed files with 118 additions and 77 deletions
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24
biology/emboss/Makefile
View file

@ -6,10 +6,11 @@
#
PORTNAME= emboss
PORTVERSION= 1.9.0
PORTVERSION= 1.9.1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
ftp://ftp.no.embnet.org/pub/EMBOSS/ \
ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
DIST_SUBDIR= ${PORTNAME}
@ -24,7 +25,6 @@ USE_GMAKE= yes
USE_LIBTOOL= yes
USE_XLIB= yes
USE_MOTIF= yes
PLIST= ${WRKDIR}/pkg-plist
PKGMESSAGE= ${WRKDIR}/pkg-message
.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc)
@ -33,29 +33,30 @@ PKGMESSAGE= ${WRKDIR}/pkg-message
CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include/gd" \
LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib"
SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \
MKDIR="${MKDIR}" \
RM="${RM}"
MKDIR="${MKDIR}" RM="${RM}"
WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY
EMNU_VERSION= 1.0.2
EMNU_VERSION= 1.0.3
MSE_VERSION= 0.0.4
TOPO_VERSION= 0.1
PHYLIP_VERSION= 3.573c
DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
.for app in EMNU MSE PHYLIP TOPO
SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}"
.if defined(WITH_${app})
APPLIST+= ${app}
PLISTS+= ${PKGDIR}/pkg-plist.${app}
${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION}
${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX}
DISTFILES+= ${${app}_DISTFILE}
PLIST_${app}= ""
.else
PLIST_${app}= "@comment "
.endif
PLIST_SUB+= PLIST_${app}=${PLIST_${app}}
.endfor
PLISTS+= ${PKGDIR}/pkg-plist
DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
pre-fetch:
@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}
@ -74,7 +75,7 @@ post-extract:
post-patch:
.for DIR in ${DOC_DIRS}
@ ${PERL} -pi.orig -e \
"s#share/\\$$\(PACKAGE\)/doc#share/doc/\\$$\(PACKAGE\)#" \
's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \
${WRKSRC}/${DIR}/Makefile.in
.endfor
@ -97,9 +98,6 @@ post-build:
${MAKE_ARGS})
.endfor
pre-install:
@ ${CAT} ${PLISTS} > ${PLIST}
post-install:
.for app in ${APPLIST}
@ (cd ${${app}_WRKSRC} && \

10
biology/emboss/distinfo
View file

@ -1,5 +1,5 @@
MD5 (emboss/EMBOSS-1.9.0.tar.gz) = f2b0ea093986df4f67428b2614583a7c
MD5 (emboss/EMNU-1.0.2.tar.gz) = 86a8ad78d25de4b56e251a266a64f46b
MD5 (emboss/MSE-0.0.4.tar.gz) = 28652ee772f31ced0e62415d8770311f
MD5 (emboss/PHYLIP-3.573c.tar.gz) = a868fbf7bbee8d97b566be6794f51eb3
MD5 (emboss/TOPO-0.1.tar.gz) = 83c76fddd2cb64d90eed4e7bb4ac0d29
MD5 (emboss/EMBOSS-1.9.1.tar.gz) = 569ff1f9f2df08928b2dfb8ae1a331b9
MD5 (emboss/EMNU-1.0.3.tar.gz) = 829dedc516e72144563d3a1a77793678
MD5 (emboss/MSE-0.0.4.tar.gz) = 83b989776fbd59e346a2f90e7dc7f266
MD5 (emboss/PHYLIP-3.573c.tar.gz) = bb1d9da41c6bfdb47828a7a9e0e40b2f
MD5 (emboss/TOPO-0.1.tar.gz) = 039b26ed333a3ba6bed20d1caf707834

2
biology/emboss/files/patch-aa
View file

@ -17,7 +17,7 @@ The port installs ${PREFIX}/etc/emboss.default.sample
+ if (!prefixRootFile)
+ {
+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
+ namInstallRoot, prefixCap, prefix);
+ namInstallRoot, prefix);
+ prefixRootFile = fopen (ajStrStr(namRootStr), "r");
+ }
+

11
biology/emboss/files/patch-configure Normal file
View file

@ -0,0 +1,11 @@
--- configure.orig Mon Jan 22 23:28:17 2001
+++ configure Thu Jan 25 19:07:33 2001
@@ -1473,7 +1473,7 @@
-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
#AC_PROG_CXX
for ac_prog in mawk gawk nawk awk

32
biology/emboss/files/patch-emboss-acd-emboss.default Normal file
View file

@ -0,0 +1,32 @@
--- emboss/acd/emboss.default.orig Mon Jan 22 23:26:54 2001
+++ emboss/acd/emboss.default Mon Jan 29 16:23:15 2001
@@ -1,9 +1,26 @@
-SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
+#####################################################
+### Configuration options for FreeBSD EMBOSS port ###
+#####################################################
-# Logfile - set this to a file that any user can append to
-# and EMBOSS applications will automatically write log information
+# This is the compiled-in default. Change only if
+# you know what you're doing!
+#
+#SET emboss_data /usr/local/share/EMBOSS/data
+# This is where your local databases reside
+# (this will differ from site to site):
+#
+SET emboss_tempdata /var/db/bio
+
+# Logfile - set this to a file that any user can append to and EMBOSS
+# applications will automatically write log information
+#
#SET emboss_logfile /packages/emboss/emboss/log
+
+
+###########################################
+### Configuration options for databases ###
+###########################################
# swissprot (Puffer fish entries)
# =========

58
biology/emboss/pkg-plist
View file

@ -1,3 +1,61 @@
%%PLIST_EMNU%%bin/emnu
%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
%%PLIST_MSE%%bin/mse
%%PLIST_MSE%%lib/libckit.a
%%PLIST_MSE%%lib/libckit.la
%%PLIST_MSE%%lib/libckit.so
%%PLIST_MSE%%lib/libckit.so.1
%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
%%PLIST_PHYLIP%%bin/eclique
%%PLIST_PHYLIP%%bin/econsense
%%PLIST_PHYLIP%%bin/econtml
%%PLIST_PHYLIP%%bin/econtrast
%%PLIST_PHYLIP%%bin/ednacomp
%%PLIST_PHYLIP%%bin/ednadist
%%PLIST_PHYLIP%%bin/ednainvar
%%PLIST_PHYLIP%%bin/ednaml
%%PLIST_PHYLIP%%bin/ednamlk
%%PLIST_PHYLIP%%bin/ednapars
%%PLIST_PHYLIP%%bin/ednapenny
%%PLIST_PHYLIP%%bin/edollop
%%PLIST_PHYLIP%%bin/edolpenny
%%PLIST_PHYLIP%%bin/efactor
%%PLIST_PHYLIP%%bin/efitch
%%PLIST_PHYLIP%%bin/egendist
%%PLIST_PHYLIP%%bin/ekitsch
%%PLIST_PHYLIP%%bin/emix
%%PLIST_PHYLIP%%bin/eneighbor
%%PLIST_PHYLIP%%bin/epenny
%%PLIST_PHYLIP%%bin/eprotdist
%%PLIST_PHYLIP%%bin/eprotpars
%%PLIST_PHYLIP%%bin/erestml
%%PLIST_PHYLIP%%bin/eseqboot
%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
%%PLIST_TOPO%%bin/topo
%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
bin/abiview
bin/acdc
bin/antigenic

2
biology/emboss/pkg-plist.EMNU
View file

@ -1,2 +0,0 @@
bin/emnu
share/EMBOSS/acd/emnu.acd

6
biology/emboss/pkg-plist.MSE
View file

@ -1,6 +0,0 @@
bin/mse
lib/libckit.a
lib/libckit.la
lib/libckit.so
lib/libckit.so.1
share/EMBOSS/acd/mse.acd

48
biology/emboss/pkg-plist.PHYLIP
View file

@ -1,48 +0,0 @@
bin/eclique
bin/econsense
bin/econtml
bin/econtrast
bin/ednacomp
bin/ednadist
bin/ednainvar
bin/ednaml
bin/ednamlk
bin/ednapars
bin/ednapenny
bin/edollop
bin/edolpenny
bin/efactor
bin/efitch
bin/egendist
bin/ekitsch
bin/emix
bin/eneighbor
bin/epenny
bin/eprotdist
bin/eprotpars
bin/erestml
bin/eseqboot
share/EMBOSS/acd/eclique.acd
share/EMBOSS/acd/econsense.acd
share/EMBOSS/acd/econtml.acd
share/EMBOSS/acd/econtrast.acd
share/EMBOSS/acd/ednacomp.acd
share/EMBOSS/acd/ednadist.acd
share/EMBOSS/acd/ednainvar.acd
share/EMBOSS/acd/ednaml.acd
share/EMBOSS/acd/ednamlk.acd
share/EMBOSS/acd/ednapars.acd
share/EMBOSS/acd/ednapenny.acd
share/EMBOSS/acd/edollop.acd
share/EMBOSS/acd/edolpenny.acd
share/EMBOSS/acd/efactor.acd
share/EMBOSS/acd/efitch.acd
share/EMBOSS/acd/egendist.acd
share/EMBOSS/acd/ekitsch.acd
share/EMBOSS/acd/emix.acd
share/EMBOSS/acd/eneighbor.acd
share/EMBOSS/acd/epenny.acd
share/EMBOSS/acd/eprotdist.acd
share/EMBOSS/acd/eprotpars.acd
share/EMBOSS/acd/erestml.acd
share/EMBOSS/acd/eseqboot.acd

2
biology/emboss/pkg-plist.TOPO
View file

@ -1,2 +0,0 @@
bin/topo
share/EMBOSS/acd/topo.acd