From owner-freebsd-ports Tue Nov 5 15: 0:32 2002 Delivered-To: freebsd-ports@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 2789C37B401 for ; Tue, 5 Nov 2002 15:00:11 -0800 (PST) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 1B77743E4A for ; Tue, 5 Nov 2002 15:00:10 -0800 (PST) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.12.6/8.12.6) with ESMTP id gA5N0Ax3027329 for ; Tue, 5 Nov 2002 15:00:10 -0800 (PST) (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.6/8.12.6/Submit) id gA5N0A4F027328; Tue, 5 Nov 2002 15:00:10 -0800 (PST) Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 156C137B401 for ; Tue, 5 Nov 2002 14:53:08 -0800 (PST) Received: from gateway.biolateral.com.au (yellow.biolateral.com.au [129.78.217.60]) by mx1.FreeBSD.org (Postfix) with ESMTP id 671E043E6E for ; Tue, 5 Nov 2002 14:53:06 -0800 (PST) (envelope-from chuynh@biolateral.com.au) Received: from oasis.bio (localhost [127.0.0.1]) by gateway.biolateral.com.au (8.12.6/8.12.6) with ESMTP id gA5MsBiH004439 for ; Wed, 6 Nov 2002 09:54:12 +1100 (EST) (envelope-from chuynh@oasis.bio) Received: (from chuynh@localhost) by oasis.bio (8.12.6/8.12.6/Submit) id gA5MsBLv004438; Wed, 6 Nov 2002 09:54:11 +1100 (EST) Message-Id: <200211052254.gA5MsBLv004438@oasis.bio> Date: Wed, 6 Nov 2002 09:54:11 +1100 (EST) From: Camson Huynh Reply-To: Camson Huynh To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Subject: ports/44957: Update Port: biology/spdbv Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >Number: 44957 >Category: ports >Synopsis: Update Port: biology/spdbv >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Tue Nov 05 15:00:09 PST 2002 >Closed-Date: >Last-Modified: >Originator: Camson Huynh >Release: FreeBSD 4.7-STABLE i386 >Organization: BioLateral Pty Ltd >Environment: System: FreeBSD oasis.bio 4.7-STABLE FreeBSD 4.7-STABLE #0: Tue Oct 29 11:56:38 EST 2002 root@oasis.bio:/usr/obj/disk/usr/src/sys/OASIS i386 >Description: Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server developped at Glaxo Welcome Experimental Research in Geneva. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. WWW: http://www.expasy.ch/spdbv/ >How-To-Repeat: >Fix: diff -ruN spdbv.orig/Makefile spdbv/Makefile --- spdbv.orig/Makefile Wed Nov 6 09:39:53 2002 +++ spdbv/Makefile Wed Nov 6 09:45:04 2002 @@ -6,7 +6,7 @@ # PORTNAME= spdbv -PORTVERSION= 37b2 +PORTVERSION= 3.7 CATEGORIES= biology MASTER_SITES= http://au.expasy.org/spdbv/program/ \ http://www.expasy.org/spdbv/program/ \ @@ -17,16 +17,18 @@ http://inn-prot.weizmann.ac.il/spdbv/program/\ http://www.usm.maine.edu/spdbv/program/ \ http://www.genebee.msu.ru/spdbv/program/ -DISTNAME= ${PORTNAME}${PORTVERSION}_IRIX_Linux +DISTNAME= ${PORTNAME}${PORTVERSION:C/\.//}-Linux MAINTAINER= chuynh@biolateral.com.au -RUN_DEPENDS= ${LINUXBASE}${X11BASE}/lib/libMesaGL.so.3:${PORTSDIR}/graphics/linux_mesa3 +RUN_DEPENDS= ${LINUXBASE}${X11BASE}/lib/libMesaGL.so.3:${PORTSDIR}/graphics/linux_mesa3 \ + ${LINUXBASE}${X11BASE}/lib/libXm.so.2:${PORTSDIR}/x11-toolkits/linux-openmotif SPDBV= SPDBV WRKSRC= ${WRKDIR}/SPDBV_DISTRIBUTION +USE_LINUX= yes NO_BUILD= yes NO_CDROM= "Must be downloaded direct from Expasy via www interface" diff -ruN spdbv.orig/distinfo spdbv/distinfo --- spdbv.orig/distinfo Wed Nov 6 09:39:53 2002 +++ spdbv/distinfo Wed Nov 6 09:45:12 2002 @@ -1 +1 @@ -MD5 (spdbv37b2_IRIX_Linux.tar.gz) = 28513cb85c8e09493d8be535e76076a3 +MD5 (spdbv37-Linux.tar.gz) = 502394bb3d12fcaad89e80cc3398b0da diff -ruN spdbv.orig/files/patch-aa spdbv/files/patch-aa --- spdbv.orig/files/patch-aa Wed Nov 6 09:39:53 2002 +++ spdbv/files/patch-aa Wed Nov 6 09:47:55 2002 @@ -1,7 +1,7 @@ ---- install.sh.orig Mon Dec 4 21:31:45 2000 -+++ install.sh Thu Dec 20 10:15:42 2001 +--- install.sh.orig Tue Nov 5 13:55:58 2002 ++++ install.sh Tue Nov 5 14:02:10 2002 @@ -7,10 +7,9 @@ - SPDBVNEEDOSbis="Linux" + SPDBVNEEDOS="Linux" SPDBVUSERDIR="$HOME" -SPDBVSHAREDIR="/usr/share" @@ -30,27 +30,27 @@ - else - abort - fi -+ echo " " -+ echo "will reinstall" ++ echo " " ++ echo "will reinstall" fi mkdir $SPDBVDEST/$SPDBVDIR #2> /dev/null if [ ! -d $SPDBVDEST/$SPDBVDIR ]; then -@@ -64,11 +51,11 @@ - chmod ugo+rx $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh +@@ -63,11 +50,11 @@ + chmod ugo+rx $SPDBVDEST/$SPDBVDIR/bin/spdbv - #try to make link from /usr/bin/spdbv to ./spdbv.sh + #try to make link from /usr/bin/spdbv to ./spdbv - if [ ! -w /usr/bin/ ]; then + if [ ! -w ${SPDBVDEST}/bin/ ]; then echo " " -- echo "Can't make a link from /usr/bin/spdbv to spdbv.sh" -+ echo "Can't make a link from ${SPDBVDEST}/bin/spdbv to spdbv.sh" +- echo "Can't make a link from /usr/bin/spdbv to $SPDBVDEST/$SPDBVDIR/bin/spdbv" ++ echo "Can't make a link from ${SPDBVDEST}/bin/spdbv to $SPDBVDEST/$SPDBVDIR/bin/spdbv" else -- ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh /usr/bin/spdbv -+ ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh ${SPDBVDEST}/bin/spdbv +- ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv /usr/bin/spdbv ++ ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv ${SPDBVDEST}/bin/spdbv fi } -@@ -82,65 +69,18 @@ +@@ -81,65 +68,18 @@ echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)" echo " " echo " " @@ -99,7 +99,7 @@ echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)" echo " " echo "Installation completed." -- echo "Start your copy of SPDBV with the script $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh" +- echo "Start your copy of SPDBV with the script $SPDBVDEST/$SPDBVDIR/bin/spdbv" echo "" echo "ENJOY SPDBV!" exit diff -ruN spdbv.orig/files/patch-ab spdbv/files/patch-ab --- spdbv.orig/files/patch-ab Wed Nov 6 09:39:53 2002 +++ spdbv/files/patch-ab Tue Nov 5 14:08:23 2002 @@ -1,20 +1,11 @@ ---- SPDBV/bin/spdbv-orig.sh.orig Thu Dec 20 10:11:25 2001 -+++ SPDBV/bin/spdbv-orig.sh Thu Dec 20 10:26:00 2001 +--- SPDBV/bin/spdbv-orig.sh.orig Tue Nov 5 14:03:36 2002 ++++ SPDBV/bin/spdbv-orig.sh Tue Nov 5 14:08:19 2002 @@ -1,6 +1,8 @@ ARCH=`uname -s` if [ $ARCH = IRIX64 ]; then ARCH=IRIX +elif [ $ARCH = FreeBSD ]; then -+ ARCH=Linux ++ ARCH=Linux fi SPDBV_TEMP=$HOME/SPDBV/temp SPDBV_DOWNLOAD=$HOME/SPDBV/download -@@ -38,7 +40,5 @@ - #xrdb -override $SPDBV_BASE/app-defaults/Spdbv - - #start the SPDBV, reroute stderr to nirvana --{ -- $SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $* --} 2> /dev/null -+$SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $* - #done. diff -ruN spdbv.orig/pkg-plist spdbv/pkg-plist --- spdbv.orig/pkg-plist Wed Nov 6 09:39:53 2002 +++ spdbv/pkg-plist Tue Nov 5 15:44:46 2002 @@ -1,185 +1,254 @@ -SPDBV/_stuff_/AlignWnd.hlp -SPDBV/_stuff_/CavitInf.hlp -SPDBV/_stuff_/CtrlPanl.hlp -SPDBV/_stuff_/DispWnd.hlp -SPDBV/_stuff_/LayerInf.hlp -SPDBV/_stuff_/RamaWnd.hlp -SPDBV/_stuff_/Rotolib.aa -SPDBV/_stuff_/Rotolib1.aa -SPDBV/_stuff_/Rotolib2.aa -SPDBV/_stuff_/SM_req.htm -SPDBV/_stuff_/SM_templ.htm +SPDBV/bin/ppov10 +SPDBV/bin/spdbv.Linux +SPDBV/bin/spdbv +SPDBV/readme.txt +SPDBV/news.txt SPDBV/_stuff_/XtalInf.hlp -SPDBV/_stuff_/_loopDB_ -SPDBV/_stuff_/crystmov.txt -SPDBV/_stuff_/crystsym.txt -SPDBV/_stuff_/default.PP -SPDBV/_stuff_/grmparam/angles.prm -SPDBV/_stuff_/grmparam/bonds.prm -SPDBV/_stuff_/grmparam/improper.prm 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