diff options
author | kris <kris@FreeBSD.org> | 2005-02-18 23:44:49 +0000 |
---|---|---|
committer | kris <kris@FreeBSD.org> | 2005-02-18 23:44:49 +0000 |
commit | ce11730ca63b2bfdd92b52e40cdc577ec691204c (patch) | |
tree | f37b198be23720d680d7ba9530cb6462b10e2dc8 /biology | |
parent | d797fb9993731e4946623d4ed61e31f12a38f0e9 (diff) | |
download | FreeBSD-ports-ce11730ca63b2bfdd92b52e40cdc577ec691204c.zip FreeBSD-ports-ce11730ca63b2bfdd92b52e40cdc577ec691204c.tar.gz |
As previously announced, remove ports that have reached their expiry date,
and the handful of ports that depended on them.
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/spdbv/Makefile | 45 | ||||
-rw-r--r-- | biology/spdbv/distinfo | 2 | ||||
-rw-r--r-- | biology/spdbv/files/patch-aa | 118 | ||||
-rw-r--r-- | biology/spdbv/files/patch-ab | 11 | ||||
-rw-r--r-- | biology/spdbv/pkg-descr | 24 | ||||
-rw-r--r-- | biology/spdbv/pkg-plist | 254 |
7 files changed, 0 insertions, 455 deletions
diff --git a/biology/Makefile b/biology/Makefile index 1e9c126..0b1acbd 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -58,7 +58,6 @@ SUBDIR += seaview SUBDIR += seqio SUBDIR += sim4 - SUBDIR += spdbv SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker diff --git a/biology/spdbv/Makefile b/biology/spdbv/Makefile deleted file mode 100644 index 27e266b..0000000 --- a/biology/spdbv/Makefile +++ /dev/null @@ -1,45 +0,0 @@ -# New ports collection makefile for: spdbv -# Date created: 15 Jan 2002 -# Whom: chuynh@biolateral.com.au -# -# $FreeBSD$ -# - -PORTNAME= spdbv -PORTVERSION= 3.7 -PORTREVISION= 1 -CATEGORIES= biology -MASTER_SITES= http://au.expasy.org/spdbv/program/ \ - http://www.expasy.org/spdbv/program/ \ - http://tw.expasy.org/spdbv/program/ \ - http://cn.expasy.org/spdbv/program/ \ - http://ca.expasy.org/spdbv/program/ \ - http://kr.expasy.org/spdbv/program/ \ - http://www.usm.maine.edu/spdbv/program/ \ - http://www.genebee.msu.ru/spdbv/program/ -DISTNAME= ${PORTNAME}${PORTVERSION:C/\.//}-Linux - -MAINTAINER= chuynh@biolateral.com.au -COMMENT= Deep View Swiss-PdbViewer is a Protein viewer and analysis tool - -RUN_DEPENDS= ${LINUXBASE}${X11BASE}/lib/libMesaGL.so.3:${PORTSDIR}/graphics/linux_mesa3 \ - ${LINUXBASE}${X11BASE}/lib/libXm.so.3:${PORTSDIR}/x11-toolkits/linux-openmotif - -SPDBV= SPDBV - -IGNORE= is incompatible with new x11-toolkits/linux-openmotif 2.2.4 -EXPIRATION_DATE=2005-02-18 -DEPRECATED= "${IGNORE}" - -WRKSRC= ${WRKDIR}/SPDBV_DISTRIBUTION - -USE_LINUX= yes -NO_BUILD= yes -NO_CDROM= "Must be downloaded direct from Expasy via www interface" - -do-install: - @cd ${WRKSRC}; ${SETENV} PREFIX=${PREFIX} ./install.sh - -# PLIST_SUB= PORTVERSION="${PORTVERSION}" - -.include <bsd.port.mk> diff --git a/biology/spdbv/distinfo b/biology/spdbv/distinfo deleted file mode 100644 index e56e68a..0000000 --- a/biology/spdbv/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -MD5 (spdbv37-Linux.tar.gz) = 502394bb3d12fcaad89e80cc3398b0da -SIZE (spdbv37-Linux.tar.gz) = 4608008 diff --git a/biology/spdbv/files/patch-aa b/biology/spdbv/files/patch-aa deleted file mode 100644 index 13565d0..0000000 --- a/biology/spdbv/files/patch-aa +++ /dev/null @@ -1,118 +0,0 @@ ---- install.sh.orig Tue Nov 5 13:55:58 2002 -+++ install.sh Tue Nov 5 14:02:10 2002 -@@ -7,10 +7,9 @@ - SPDBVNEEDOS="Linux" - - SPDBVUSERDIR="$HOME" --SPDBVSHAREDIR="/usr/share" - SPDBVDIR="SPDBV" - SPDBVSTUFF="_stuff_" --SPDBVDEST="" -+SPDBVDEST="${PREFIX}" - SPDBVOSVERSION=`uname -r` - SPDBVOS=`uname -s` - if [ $SPDBVOS = IRIX64 ]; then -@@ -27,20 +26,8 @@ - echo "Will install the shared files in $SPDBVDEST." - if [ -d $SPDBVDEST/$SPDBVDIR ]; then - echo "Shared files are already installed on this system." -- echo "Delete old files and reinstall (Y/N)?" -- read INP -- if [ $INP = "Y" -o $INP = "y" ]; then -- echo " " -- echo "will reinstall" -- if [ -w $SPDBVDEST/$SPDBVDIR ]; then -- rm -r $SPDBVDEST/$SPDBVDIR -- else -- echo "Could not delete shared files." -- abort -- fi -- else -- abort -- fi -+ echo " " -+ echo "will reinstall" - fi - mkdir $SPDBVDEST/$SPDBVDIR #2> /dev/null - if [ ! -d $SPDBVDEST/$SPDBVDIR ]; then -@@ -63,11 +50,11 @@ - chmod ugo+rx $SPDBVDEST/$SPDBVDIR/bin/spdbv - - #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 $SPDBVDEST/$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 /usr/bin/spdbv -+ ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv ${SPDBVDEST}/bin/spdbv - fi - } - -@@ -81,65 +68,18 @@ - echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)" - echo " " - echo " " -- echo " Please follow the instructions below." -- echo " " -- echo "Where do you want me to install the files:" -- echo "globally in /usr/share/SPDBV -> G" -- echo "or just locally in ~/SPDBV -> L" -- echo "something different -> O" -- echo "(G/L/O)?" -- read DEST -- -- SPDBVDEST="" -- if [ $DEST = "G" -o $DEST = "g" ]; then -- SPDBVDEST=$SPDBVSHAREDIR -- elif [ $DEST = "L" -o $DEST = "l" ]; then -- SPDBVDEST=$SPDBVUSERDIR -- elif [ $DEST = "O" -o $DEST = "o" ]; then -- echo "enter target Path where to install directory SPDBV:" -- read SPDBVDEST -- fi -- -- if [ -z $SPDBVDEST ]; then -- echo "" -- echo "$SPDBVDEST is not a valid answer. 1" -- echo "" -- echo "continue .. hit any key" -- read DEST -- mainmenu -- fi -- if [ ! '(' -d $SPDBVDEST ')' ]; then -- echo "" -- echo "$SPDBVDEST is not a valid answer. 2" -- echo "" -- echo "continue .. hit any key" -- read DEST -- mainmenu -- fi - - makesharedinst - --# clear -- - echo " " - echo " SPDBV - Swiss PDB Viewer" - echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)" - echo " " - echo "Installation completed." -- echo "Start your copy of SPDBV with the script $SPDBVDEST/$SPDBVDIR/bin/spdbv" - echo "" - echo "ENJOY SPDBV!" - exit - } -- --# test for the right os --if [ $SPDBVOS != $SPDBVNEEDOS ]; then -- if [ $SPDBVOS != $SPDBVNEEDOSbis ]; then -- echo "SPDBV $SPDBVVERSION ($SPDBVNEEDOS) is intended to run on hardware under $SPDBVNEEDOS." -- abort -- exit -- fi --fi - - # start up the mainmenu - mainmenu diff --git a/biology/spdbv/files/patch-ab b/biology/spdbv/files/patch-ab deleted file mode 100644 index 04dd22a..0000000 --- a/biology/spdbv/files/patch-ab +++ /dev/null @@ -1,11 +0,0 @@ ---- 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 [ $ARCH = FreeBSD ]; then -+ ARCH=Linux - fi - SPDBV_TEMP=$HOME/SPDBV/temp - SPDBV_DOWNLOAD=$HOME/SPDBV/download diff --git a/biology/spdbv/pkg-descr b/biology/spdbv/pkg-descr deleted file mode 100644 index c35f6ac..0000000 --- a/biology/spdbv/pkg-descr +++ /dev/null @@ -1,24 +0,0 @@ -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/ diff --git a/biology/spdbv/pkg-plist b/biology/spdbv/pkg-plist deleted file mode 100644 index 8cc0e4f..0000000 --- a/biology/spdbv/pkg-plist +++ /dev/null @@ -1,254 +0,0 @@ -SPDBV/bin/ppov10 -SPDBV/bin/spdbv.Linux -SPDBV/bin/spdbv -SPDBV/readme.txt -SPDBV/news.txt -SPDBV/_stuff_/XtalInf.hlp -SPDBV/_stuff_/CavitInf.hlp -SPDBV/_stuff_/grmparam/CVS/Tag -SPDBV/_stuff_/grmparam/CVS/Root -SPDBV/_stuff_/grmparam/CVS/Entries -SPDBV/_stuff_/grmparam/CVS/Repository -SPDBV/_stuff_/grmparam/torsion.prm -SPDBV/_stuff_/grmparam/nbondsel.prm -SPDBV/_stuff_/grmparam/bonds.prm -SPDBV/_stuff_/grmparam/nonbonds.prm -SPDBV/_stuff_/grmparam/improper.prm -SPDBV/_stuff_/grmparam/angles.prm -SPDBV/_stuff_/gifs/getacro.gif -SPDBV/_stuff_/gifs/tips.gif -SPDBV/_stuff_/gifs/userguide.gif -SPDBV/_stuff_/gifs/feedback.gif -SPDBV/_stuff_/gifs/artgallery.gif -SPDBV/_stuff_/gifs/tutorial.gif -SPDBV/_stuff_/gifs/download.gif -SPDBV/_stuff_/gifs/references.gif -SPDBV/_stuff_/gifs/mirror.gif -SPDBV/_stuff_/gifs/index.gif -SPDBV/_stuff_/gifs/logo.gif -SPDBV/_stuff_/text/stereo.htm -SPDBV/_stuff_/text/loop.htm -SPDBV/_stuff_/text/fabp.htm -SPDBV/_stuff_/text/modeling.htm -SPDBV/_stuff_/text/pattern.htm -SPDBV/_stuff_/text/rama.htm -SPDBV/_stuff_/text/faq.htm -SPDBV/_stuff_/text/torsion.htm -SPDBV/_stuff_/text/templ_1.html -SPDBV/_stuff_/text/povscene.htm -SPDBV/_stuff_/text/build.htm -SPDBV/_stuff_/text/gromo_pl.htm -SPDBV/_stuff_/text/activsit.htm -SPDBV/_stuff_/text/tips.htm -SPDBV/_stuff_/text/refs.htm -SPDBV/_stuff_/text/disclaim.htm -SPDBV/_stuff_/text/render.htm -SPDBV/_stuff_/text/tools.htm -SPDBV/_stuff_/text/epot.htm -SPDBV/_stuff_/text/prefs.htm -SPDBV/_stuff_/text/color.htm -SPDBV/_stuff_/text/gallery_local.htm -SPDBV/_stuff_/text/files.htm -SPDBV/_stuff_/text/superpos.htm -SPDBV/_stuff_/text/feedback.htm -SPDBV/_stuff_/text/cshrc.htm -SPDBV/_stuff_/text/rendcomp.htm -SPDBV/_stuff_/text/pov.htm -SPDBV/_stuff_/text/display.htm -SPDBV/_stuff_/text/hew.htm -SPDBV/_stuff_/text/gallery.htm -SPDBV/_stuff_/text/energy.htm -SPDBV/_stuff_/text/disclaim_local.htm -SPDBV/_stuff_/text/mutation.htm -SPDBV/_stuff_/text/ribbon.htm -SPDBV/_stuff_/text/transfo.htm -SPDBV/_stuff_/text/moving.htm -SPDBV/_stuff_/text/select.htm -SPDBV/_stuff_/text/edmtut.htm -SPDBV/_stuff_/text/surface.htm -SPDBV/_stuff_/text/gromotut.htm -SPDBV/_stuff_/text/ctrlpanl.htm -SPDBV/_stuff_/text/tutorial.htm -SPDBV/_stuff_/text/distort.htm -SPDBV/_stuff_/text/selmenu.htm -SPDBV/_stuff_/text/toolmenu.htm -SPDBV/_stuff_/text/xsymtut.htm -SPDBV/_stuff_/text/server.htm -SPDBV/_stuff_/text/mirror.htm -SPDBV/_stuff_/text/rotolib.htm -SPDBV/_stuff_/text/edm.htm -SPDBV/_stuff_/text/main.htm -SPDBV/_stuff_/text/index.htm -SPDBV/_stuff_/text/phipsi.htm -SPDBV/_stuff_/manual.htm -SPDBV/_stuff_/crystsym.txt -SPDBV/_stuff_/SM_templ.htm -SPDBV/_stuff_/grmtopol/CVS/Tag -SPDBV/_stuff_/grmtopol/CVS/Root -SPDBV/_stuff_/grmtopol/CVS/Entries -SPDBV/_stuff_/grmtopol/CVS/Repository -SPDBV/_stuff_/grmtopol/ATP.tpl -SPDBV/_stuff_/grmtopol/ASP.tpl -SPDBV/_stuff_/grmtopol/TRP.tpl -SPDBV/_stuff_/grmtopol/SEP.tpl -SPDBV/_stuff_/grmtopol/HISA.tpl -SPDBV/_stuff_/grmtopol/HIS1.tpl -SPDBV/_stuff_/grmtopol/CYS1.tpl -SPDBV/_stuff_/grmtopol/CU1.tpl -SPDBV/_stuff_/grmtopol/ALA.tpl -SPDBV/_stuff_/grmtopol/NA.tpl -SPDBV/_stuff_/grmtopol/HISB.tpl -SPDBV/_stuff_/grmtopol/CYS2.tpl -SPDBV/_stuff_/grmtopol/SO42.tpl -SPDBV/_stuff_/grmtopol/CA2.tpl -SPDBV/_stuff_/grmtopol/THR.tpl -SPDBV/_stuff_/grmtopol/TYR.tpl -SPDBV/_stuff_/grmtopol/SER.tpl -SPDBV/_stuff_/grmtopol/LYS.tpl -SPDBV/_stuff_/grmtopol/CYS.tpl -SPDBV/_stuff_/grmtopol/OXT.tpl -SPDBV/_stuff_/grmtopol/MET.tpl -SPDBV/_stuff_/grmtopol/HHT.tpl 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