Revision: 76582 http://trac.macports.org/changeset/76582 Author: ryandesign@macports.org Date: 2011-02-28 13:16:04 -0800 (Mon, 28 Feb 2011) Log Message: ----------- arb: update to 5.2, use a distfile instead of fetching from Subversion, add .xmodmap setup; see #28276 Modified Paths: -------------- trunk/dports/science/arb/Portfile trunk/dports/science/arb/files/arb_macsetup Added Paths: ----------- trunk/dports/science/arb/files/arb_intro.fig.diff Modified: trunk/dports/science/arb/Portfile =================================================================== --- trunk/dports/science/arb/Portfile 2011-02-28 21:09:37 UTC (rev 76581) +++ trunk/dports/science/arb/Portfile 2011-02-28 21:16:04 UTC (rev 76582) @@ -4,9 +4,8 @@ PortSystem 1.0 name arb -version 5.1 epoch 1 -revision 2 +version 5.2 categories science maintainers me.com:matt.cottrell platforms darwin @@ -24,15 +23,15 @@ (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment \ for sequence data. Nucleic Acids Research. 32:1363-1371. -fetch.type svn -svn.url http://svn.mikro.biologie.tu-muenchen.de/svn/branches/stable_5.0 -svn.revision 6215 -svn.method checkout -#fetch.user coder -#fetch.password gimmeARBsource -#work around until ticket #21232 is resolved -svn.args --username coder --password gimmeARBsource +master_sites http://download.arb-home.de/release/arb_${version}/ +distname arbsrc +extract.suffix .tgz +dist_subdir ${name}/${version} +worksrcdir arbsrc_6779 +checksums sha1 4ee493a16ece5231d46ed1071407c06e733d67c8 \ + rmd160 d9d99d0ebadaa293091ff93f6ca588b2321bd8b0 + depends_build port:imake \ port:makedepend @@ -53,10 +52,9 @@ patch-ARB-makefile.diff \ patch-ARB-RNA3D_GlobalHeader.hxx.diff \ patch-ARB-DARWIN.pl.diff \ - patch-ARB-glpng.diff + patch-ARB-glpng.diff \ + arb_intro.fig.diff -worksrcdir stable_5.0 - configure { reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \ ${worksrcpath}/util/arb_check_build_env.pl \ @@ -119,8 +117,6 @@ universal_variant no post-activate { - system "rm -rf `find ${prefix}/share/arb -type d -name .svn`" - # Provide users with copies of the default configuration and macros # if the user doesn't already have them. if {![file exists ${prefix}/share/arb/lib/arb_tcp.dat]} { @@ -143,11 +139,11 @@ You have two options (A is easier, B is more difficult): -A) Open a new terminal window and type arb_macsetup to set up your environment automatically +A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically. This script also enables keyboard shortcuts used in the sequence editor. or -B) Follow the steps below: +B) More difficult - follow the steps below: 1) bash users add the following lines to your ~/.profile or to your ~/.bashrc @@ -166,7 +162,21 @@ enter the following command: source ~/.cshrc +3) +create a text file in your home folder called .xmodmap that contains the text below: + +clear Mod1 +clear Mod2 +keycode 63 = Mode_switch +keycode 66 = Meta_L +keycode 69 = Meta_R +add Mod1 = Meta_L Meta_R +add Mod2 = Mode_switch + C) +to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup + +D) type arb to start ARB A demo data base is located at ${prefix}/share/arb/demo.arb Added: trunk/dports/science/arb/files/arb_intro.fig.diff =================================================================== --- trunk/dports/science/arb/files/arb_intro.fig.diff (rev 0) +++ trunk/dports/science/arb/files/arb_intro.fig.diff 2011-02-28 21:16:04 UTC (rev 76582) @@ -0,0 +1,88 @@ +--- arb_intro.fig.orig 2011-02-04 01:01:34.000000000 -0300 ++++ lib/pictures/arb_intro.fig 2010-10-24 18:34:25.000000000 -0300 +@@ -1,4 +1,4 @@ +-#FIG 3.2 ++#FIG 3.2 Produced by xfig version 3.2.5 + Landscape + Center + Metric +@@ -8,18 +8,18 @@ + -2 + 1200 2 + 6 8010 5175 9315 5445 +-4 0 -1 0 0 18 12 0.0000 4 135 495 8025 5340 Suffix\001 +-4 0 -1 0 0 18 12 0.0000 4 180 495 8550 5415 $filter\001 +-4 2 -1 0 0 18 12 0.0000 4 180 720 9300 5415 $to:filter\001 ++4 0 -1 0 0 18 12 0.0000 4 165 570 8025 5340 Suffix\001 ++4 0 -1 0 0 18 12 0.0000 4 210 585 8550 5415 $filter\001 ++4 2 -1 0 0 18 12 0.0000 4 210 870 9300 5415 $to:filter\001 + -6 + 6 2655 2025 8235 2295 + 2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2 + 2700 2250 8190 2250 +-4 1 -1 0 0 18 14 0.0000 4 210 5070 5400 2175 ARB - A Software Environment for Sequence Data\001 ++4 1 -1 0 0 18 14 0.0000 4 240 5925 5400 2175 ARB - A Software Environment for Sequence Data\001 + -6 + 6 1800 10890 9090 11250 +-4 0 -1 0 0 18 10 0.0000 4 135 7095 1800 11025 Y:Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar et al.\001 +-4 0 -1 0 0 18 10 0.0000 4 135 7260 1800 11205 Y:ARB: a software environment for sequence data. Nucleic Acids Research. 2004. 32(4):1363-1371.\001 ++4 0 -1 0 0 18 10 0.0000 4 150 7335 1800 11025 Y:Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar et al.\001 ++4 0 -1 0 0 18 10 0.0000 4 150 7395 1800 11205 Y:ARB: a software environment for sequence data. Nucleic Acids Research. 2004. 32(4):1363-1371.\001 + -6 + 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1 + 1170 540 +@@ -29,28 +29,29 @@ + 1350 4950 1350 4230 9090 4230 + 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1 + 9630 11340 +-4 0 -1 0 0 18 12 0.0000 4 180 570 1425 1050 $close\001 +-4 2 -1 0 0 18 12 0.0000 4 195 465 9450 1050 $help\001 +-4 2 -1 0 0 18 12 0.0000 4 180 945 9375 9990 $to:XY:box\001 +-4 0 -1 0 0 18 12 0.0000 4 195 840 9150 10440 $Y:expert\001 +-4 0 -1 0 0 18 12 0.0000 4 180 420 1500 5865 $box\001 +-4 0 -1 0 0 18 12 0.0000 4 195 2970 1500 5340 Existing Files (f) and Directories (D)\001 +-4 0 -1 0 0 18 12 0.0000 4 180 540 1620 10395 $Y:old\001 +-4 0 -1 0 0 18 12 0.0000 4 180 540 4725 10388 $Y:del\001 +-4 0 -1 0 0 18 12 0.0000 4 195 1290 1620 4725 $new_complex\001 +-4 0 -1 0 0 18 12 0.0000 4 195 660 4455 4725 $merge\001 +-4 1 -1 0 0 18 12 0.0000 4 150 750 7140 2865 Authors:\001 +-4 1 -1 0 0 18 12 0.0000 4 195 465 5265 945 $logo\001 +-4 1 -1 0 0 18 12 0.0000 4 195 2055 2745 3870 http://www.arb-home.de/\001 +-4 1 -1 0 0 18 12 0.0000 4 195 915 2745 2970 $copyright\001 +-4 1 -1 0 0 18 12 0.0000 4 195 2370 2745 3150 Department of Microbiology\001 +-4 1 -1 0 0 18 10 0.0000 4 135 2265 2745 3375 Technical University of Munich\001 +-4 1 -1 0 0 18 10 0.0000 4 135 675 2745 3555 Germany\001 +-4 1 -1 0 0 18 11 0.0000 4 150 2070 7140 3345 Harald Meier, Yadhukumar\001 +-4 1 -1 0 0 18 12 0.0000 4 195 3915 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001 +-4 1 -1 0 0 18 10 0.0000 4 105 2070 7140 3960 Lead tester: F. O. Gloeckner\001 +-4 1 -1 0 0 18 10 0.0000 4 135 3615 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001 +-4 1 -1 0 0 18 10 0.0000 4 135 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001 +-4 1 -1 0 0 18 12 0.0000 4 180 750 5265 2610 $version\001 +-4 0 -1 0 0 18 12 0.0000 4 195 1890 7350 10365 Y:Enable Expert Mode\001 +-4 0 -1 0 0 18 10 0.0000 4 135 2130 1440 10800 Y:If you use ARB, please cite\001 ++4 0 -1 0 0 18 12 0.0000 4 210 675 1425 1050 $close\001 ++4 2 -1 0 0 18 12 0.0000 4 225 570 9450 1050 $help\001 ++4 2 -1 0 0 18 12 0.0000 4 210 1140 9375 9990 $to:XY:box\001 ++4 0 -1 0 0 18 12 0.0000 4 225 990 9150 10440 $Y:expert\001 ++4 0 -1 0 0 18 12 0.0000 4 210 495 1500 5865 $box\001 ++4 0 -1 0 0 18 12 0.0000 4 210 3690 1500 5340 Existing Files (f) and Directories (D)\001 ++4 0 -1 0 0 18 12 0.0000 4 210 675 1620 10395 $Y:old\001 ++4 0 -1 0 0 18 12 0.0000 4 210 660 4725 10388 $Y:del\001 ++4 0 -1 0 0 18 12 0.0000 4 225 1500 1620 4725 $new_complex\001 ++4 0 -1 0 0 18 12 0.0000 4 225 765 4455 4725 $merge\001 ++4 1 -1 0 0 18 12 0.0000 4 165 915 7140 2865 Authors:\001 ++4 1 -1 0 0 18 12 0.0000 4 225 585 5265 945 $logo\001 ++4 1 -1 0 0 18 12 0.0000 4 210 2475 2745 3870 http://www.arb-home.de/\001 ++4 1 -1 0 0 18 12 0.0000 4 210 2910 2745 3150 Department of Microbiology\001 ++4 1 -1 0 0 18 10 0.0000 4 150 2295 2745 3375 Technical University of Munich\001 ++4 1 -1 0 0 18 10 0.0000 4 150 675 2745 3555 Germany\001 ++4 1 -1 0 0 18 11 0.0000 4 165 2340 7140 3345 Harald Meier, Yadhukumar\001 ++4 1 -1 0 0 18 12 0.0000 4 210 4800 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001 ++4 1 -1 0 0 18 10 0.0000 4 150 3660 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001 ++4 1 -1 0 0 18 10 0.0000 4 150 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001 ++4 1 -1 0 0 18 12 0.0000 4 210 900 5265 2610 $version\001 ++4 0 -1 0 0 18 12 0.0000 4 210 2295 7350 10365 Y:Enable Expert Mode\001 ++4 0 -1 0 0 18 10 0.0000 4 150 2190 1440 10800 Y:If you use ARB, please cite\001 ++4 1 -1 0 0 18 10 0.0000 4 120 2085 7110 3960 Lead tester: F. O. Gloeckner\001 ++4 1 -1 0 0 18 12 0.0000 4 225 1125 2745 2970 $copyright\001 ++4 1 -1 0 0 18 12 0.0000 4 210 3600 7155 4185 Mac OS X port: Matthew T. Cottrell\001 Modified: trunk/dports/science/arb/files/arb_macsetup =================================================================== --- trunk/dports/science/arb/files/arb_macsetup 2011-02-28 21:09:37 UTC (rev 76581) +++ trunk/dports/science/arb/files/arb_macsetup 2011-02-28 21:16:04 UTC (rev 76582) @@ -29,11 +29,11 @@ # # This is the arb_macsetup script -# Use it to set the ARBHOME and PATH variables after installing ARB using MacPorts. +# Use it to set the ARBHOME and PATH variables and to install a .xmodmap file after installing ARB using MacPorts. # Derived from the MacPorts postflight script # Provided by: Matthew Cottrell -# October 1, 2009 +# January 31, 2011 # Abstraction variables: PREFIX=@@PREFIX@@ @@ -42,6 +42,7 @@ MANPAGES=${PREFIX}/share/man TIMESTAMP=$(date +"%Y-%m-%d_at_%H:%M:%S") BACKUP_SUFFIX=macports-saved_${TIMESTAMP} +XMODMAP_FILE=xmodmap OUR_STRING="ARB Installer addition on ${TIMESTAMP}" # Determine the user's shell, in order to choose an appropriate configuration file we'll be tweaking. @@ -104,6 +105,21 @@ echo "An appropriate ${1} variable has been added to your shell environment by the ${3} installer." } +function write_xmodmap_setting () { + if [ -f ${HOME}/.${XMODMAP_FILE} ] && ! grep "${OUR_STRING}" ${HOME}/.${XMODMAP_FILE} > /dev/null; then + echo "Backing up your ${HOME}/.${XMODMAP_FILE} keyboard confguration file as ${HOME}/.${XMODMAP_FILE}.${BACKUP_SUFFIX} before adapting it for ARB." + /bin/cp -fp ${HOME}/.${XMODMAP_FILE} "${HOME}/.${XMODMAP_FILE}.${BACKUP_SUFFIX}" || { + echo "An attempt to backup your original configuration file failed! Please set your ARB compatible environment manually." + + exit 1 + } + echo -e "\n##\n# Your previous ${HOME}/.${XMODMAP_FILE} file was backed up as ${HOME}/.${XMODMAP_FILE}.${BACKUP_SUFFIX}\n##" >> ${HOME}/.${XMODMAP_FILE} + fi + echo -e "${1}\n${2}\n${3}\n${4}\n${5}\n${6}\n${7}\n" > ${HOME}/.${XMODMAP_FILE} + chown ${USER} ${HOME}/.${XMODMAP_FILE} || echo "Warning: unable to adapt permissions on your ${HOME}/.${XMODMAP_FILE} shell configuration file!" + echo "An appropriate xmodmap file has been added to your home folder by the ${8} installer." +} + # Confirm that MacPorts has been configured for this user: if ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv PATH" | grep ${PREFIX} > /dev/null; then echo "Your shell already has the right PATH environment variable for use with MacPorts!" @@ -148,6 +164,9 @@ write_setting ARBHOME "${PREFIX}/share/arb" ARB fi +#write the .xmodmap file for easy keyboard shortcutsin the ARB sequence editor +write_xmodmap_setting "clear Mod1" "clear Mod2" "keycode 63 = Mode_switch" "keycode 66 = Meta_L" "keycode 69 = Meta_R" "add Mod1 = Meta_L Meta_R" "add Mod2 = Mode_switch" ARB + # arb_setenv script is done with its job - exit gracefully! echo "" echo "You have succesfully installed ARB"