diff options
Diffstat (limited to 'biology')
-rw-r--r-- | biology/emboss/Makefile | 24 | ||||
-rw-r--r-- | biology/emboss/distinfo | 10 | ||||
-rw-r--r-- | biology/emboss/files/patch-aa | 2 | ||||
-rw-r--r-- | biology/emboss/files/patch-configure | 11 | ||||
-rw-r--r-- | biology/emboss/files/patch-emboss-acd-emboss.default | 32 | ||||
-rw-r--r-- | biology/emboss/pkg-plist | 58 | ||||
-rw-r--r-- | biology/emboss/pkg-plist.EMNU | 2 | ||||
-rw-r--r-- | biology/emboss/pkg-plist.MSE | 6 | ||||
-rw-r--r-- | biology/emboss/pkg-plist.PHYLIP | 48 | ||||
-rw-r--r-- | biology/emboss/pkg-plist.TOPO | 2 |
10 files changed, 118 insertions, 77 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 23e0b1f66e36..5d97534f4eb3 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -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} && \ diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index fce228f6c4c0..c4a6dc2e7ca1 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -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 diff --git a/biology/emboss/files/patch-aa b/biology/emboss/files/patch-aa index f4b1bc46f7a1..d8bdbf96f9fb 100644 --- a/biology/emboss/files/patch-aa +++ b/biology/emboss/files/patch-aa @@ -17,7 +17,7 @@ The port installs ${PREFIX}/etc/emboss.default.sample + if (!prefixRootFile) + { + ajFmtPrintS (&namRootStr, "%s/etc/%s.default", -+ namInstallRoot, prefixCap, prefix); ++ namInstallRoot, prefix); + prefixRootFile = fopen (ajStrStr(namRootStr), "r"); + } + diff --git a/biology/emboss/files/patch-configure b/biology/emboss/files/patch-configure new file mode 100644 index 000000000000..da46a3c60faa --- /dev/null +++ b/biology/emboss/files/patch-configure @@ -0,0 +1,11 @@ +--- configure.orig Mon Jan 22 23:28:17 2001 ++++ configure Thu Jan 25 19:07:33 2001 +@@ -1473,7 +1473,7 @@ + + + +-AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" ++AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\"" + + #AC_PROG_CXX + for ac_prog in mawk gawk nawk awk diff --git a/biology/emboss/files/patch-emboss-acd-emboss.default b/biology/emboss/files/patch-emboss-acd-emboss.default new file mode 100644 index 000000000000..8311f5b23837 --- /dev/null +++ b/biology/emboss/files/patch-emboss-acd-emboss.default @@ -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) + # ========= diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index 1cba313f1bd0..426f0514ed51 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -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 diff --git a/biology/emboss/pkg-plist.EMNU b/biology/emboss/pkg-plist.EMNU deleted file mode 100644 index fcb7fe6fe4a6..000000000000 --- a/biology/emboss/pkg-plist.EMNU +++ /dev/null @@ -1,2 +0,0 @@ -bin/emnu -share/EMBOSS/acd/emnu.acd diff --git a/biology/emboss/pkg-plist.MSE b/biology/emboss/pkg-plist.MSE deleted file mode 100644 index eaa15866ab0a..000000000000 --- a/biology/emboss/pkg-plist.MSE +++ /dev/null @@ -1,6 +0,0 @@ -bin/mse -lib/libckit.a -lib/libckit.la -lib/libckit.so -lib/libckit.so.1 -share/EMBOSS/acd/mse.acd diff --git a/biology/emboss/pkg-plist.PHYLIP b/biology/emboss/pkg-plist.PHYLIP deleted file mode 100644 index a654ca4542ca..000000000000 --- a/biology/emboss/pkg-plist.PHYLIP +++ /dev/null @@ -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 diff --git a/biology/emboss/pkg-plist.TOPO b/biology/emboss/pkg-plist.TOPO deleted file mode 100644 index 3be9738c819f..000000000000 --- a/biology/emboss/pkg-plist.TOPO +++ /dev/null @@ -1,2 +0,0 @@ -bin/topo -share/EMBOSS/acd/topo.acd |