Ticket #28276: arb-proposed-5.2-update.diff

File arb-proposed-5.2-update.diff, 11.9 KB (added by ryandesign (Ryan Carsten Schmidt), 13 years ago)

proposed patch to update to 5.2

  • files/arb_macsetup

     
    2929#
    3030
    3131# This is the arb_macsetup script
    32 # Use it to set the ARBHOME and PATH variables after installing ARB using MacPorts.
     32# Use it to set the ARBHOME and PATH variables and to install a .xmodmap file after installing ARB using MacPorts.
    3333
    3434# Derived from the MacPorts postflight script
    3535# Provided by: Matthew Cottrell
    36 # October 1, 2009
     36# January 31, 2011
    3737
    3838# Abstraction variables:
    3939PREFIX=@@PREFIX@@
    … …  
    4242MANPAGES=${PREFIX}/share/man
    4343TIMESTAMP=$(date +"%Y-%m-%d_at_%H:%M:%S")
    4444BACKUP_SUFFIX=macports-saved_${TIMESTAMP}
     45XMODMAP_FILE=xmodmap
    4546OUR_STRING="ARB Installer addition on ${TIMESTAMP}"
    4647
    4748# Determine the user's shell, in order to choose an appropriate configuration file we'll be tweaking.
    … …  
    104105    echo "An appropriate ${1} variable has been added to your shell environment by the ${3} installer."
    105106}
    106107
     108function write_xmodmap_setting () {
     109    if [ -f ${HOME}/.${XMODMAP_FILE} ] && ! grep "${OUR_STRING}" ${HOME}/.${XMODMAP_FILE} > /dev/null; then
     110        echo "Backing up your ${HOME}/.${XMODMAP_FILE} keyboard confguration file as ${HOME}/.${XMODMAP_FILE}.${BACKUP_SUFFIX} before adapting it for ARB."
     111        /bin/cp -fp ${HOME}/.${XMODMAP_FILE} "${HOME}/.${XMODMAP_FILE}.${BACKUP_SUFFIX}" || {
     112            echo "An attempt to backup your original configuration file failed! Please set your ARB compatible environment manually."
     113           
     114            exit 1
     115        }
     116        echo -e "\n##\n# Your previous ${HOME}/.${XMODMAP_FILE} file was backed up as ${HOME}/.${XMODMAP_FILE}.${BACKUP_SUFFIX}\n##" >> ${HOME}/.${XMODMAP_FILE}
     117    fi
     118    echo -e "${1}\n${2}\n${3}\n${4}\n${5}\n${6}\n${7}\n" > ${HOME}/.${XMODMAP_FILE}
     119    chown ${USER} ${HOME}/.${XMODMAP_FILE} || echo "Warning: unable to adapt permissions on your ${HOME}/.${XMODMAP_FILE} shell configuration file!"
     120    echo "An appropriate xmodmap file has been added to your home folder by the ${8} installer."
     121}
     122
    107123# Confirm that MacPorts has been configured for this user:
    108124if ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv PATH" | grep ${PREFIX} > /dev/null; then
    109125    echo "Your shell already has the right PATH environment variable for use with MacPorts!"
    … …  
    148164        write_setting ARBHOME "${PREFIX}/share/arb" ARB
    149165fi
    150166
     167#write the .xmodmap file for easy keyboard shortcutsin the ARB sequence editor
     168write_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
     169
    151170# arb_setenv script is done with its job - exit gracefully!
    152171echo ""
    153172echo "You have succesfully installed ARB"

  • files/arb_intro.fig.diff

     
     1--- arb_intro.fig.orig  2011-02-04 01:01:34.000000000 -0300
     2+++ lib/pictures/arb_intro.fig  2010-10-24 18:34:25.000000000 -0300
     3@@ -1,4 +1,4 @@
     4-#FIG 3.2
     5+#FIG 3.2  Produced by xfig version 3.2.5
     6 Landscape
     7 Center
     8 Metric
     9@@ -8,18 +8,18 @@
     10 -2
     11 1200 2
     12 6 8010 5175 9315 5445
     13-4 0 -1 0 0 18 12 0.0000 4 135 495 8025 5340 Suffix\001
     14-4 0 -1 0 0 18 12 0.0000 4 180 495 8550 5415 $filter\001
     15-4 2 -1 0 0 18 12 0.0000 4 180 720 9300 5415 $to:filter\001
     16+4 0 -1 0 0 18 12 0.0000 4 165 570 8025 5340 Suffix\001
     17+4 0 -1 0 0 18 12 0.0000 4 210 585 8550 5415 $filter\001
     18+4 2 -1 0 0 18 12 0.0000 4 210 870 9300 5415 $to:filter\001
     19 -6
     20 6 2655 2025 8235 2295
     21 2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
     22         2700 2250 8190 2250
     23-4 1 -1 0 0 18 14 0.0000 4 210 5070 5400 2175 ARB - A Software Environment for Sequence Data\001
     24+4 1 -1 0 0 18 14 0.0000 4 240 5925 5400 2175 ARB - A Software Environment for Sequence Data\001
     25 -6
     26 6 1800 10890 9090 11250
     27-4 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
     28-4 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
     29+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
     30+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
     31 -6
     32 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1
     33         1170 540
     34@@ -29,28 +29,29 @@
     35         1350 4950 1350 4230 9090 4230
     36 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1
     37         9630 11340
     38-4 0 -1 0 0 18 12 0.0000 4 180 570 1425 1050 $close\001
     39-4 2 -1 0 0 18 12 0.0000 4 195 465 9450 1050 $help\001
     40-4 2 -1 0 0 18 12 0.0000 4 180 945 9375 9990 $to:XY:box\001
     41-4 0 -1 0 0 18 12 0.0000 4 195 840 9150 10440 $Y:expert\001
     42-4 0 -1 0 0 18 12 0.0000 4 180 420 1500 5865 $box\001
     43-4 0 -1 0 0 18 12 0.0000 4 195 2970 1500 5340 Existing Files (f) and Directories (D)\001
     44-4 0 -1 0 0 18 12 0.0000 4 180 540 1620 10395 $Y:old\001
     45-4 0 -1 0 0 18 12 0.0000 4 180 540 4725 10388 $Y:del\001
     46-4 0 -1 0 0 18 12 0.0000 4 195 1290 1620 4725 $new_complex\001
     47-4 0 -1 0 0 18 12 0.0000 4 195 660 4455 4725 $merge\001
     48-4 1 -1 0 0 18 12 0.0000 4 150 750 7140 2865 Authors:\001
     49-4 1 -1 0 0 18 12 0.0000 4 195 465 5265 945 $logo\001
     50-4 1 -1 0 0 18 12 0.0000 4 195 2055 2745 3870 http://www.arb-home.de/\001
     51-4 1 -1 0 0 18 12 0.0000 4 195 915 2745 2970 $copyright\001
     52-4 1 -1 0 0 18 12 0.0000 4 195 2370 2745 3150 Department of Microbiology\001
     53-4 1 -1 0 0 18 10 0.0000 4 135 2265 2745 3375 Technical University of Munich\001
     54-4 1 -1 0 0 18 10 0.0000 4 135 675 2745 3555 Germany\001
     55-4 1 -1 0 0 18 11 0.0000 4 150 2070 7140 3345 Harald Meier, Yadhukumar\001
     56-4 1 -1 0 0 18 12 0.0000 4 195 3915 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001
     57-4 1 -1 0 0 18 10 0.0000 4 105 2070 7140 3960 Lead tester: F. O. Gloeckner\001
     58-4 1 -1 0 0 18 10 0.0000 4 135 3615 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001
     59-4 1 -1 0 0 18 10 0.0000 4 135 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001
     60-4 1 -1 0 0 18 12 0.0000 4 180 750 5265 2610 $version\001
     61-4 0 -1 0 0 18 12 0.0000 4 195 1890 7350 10365 Y:Enable Expert Mode\001
     62-4 0 -1 0 0 18 10 0.0000 4 135 2130 1440 10800 Y:If you use ARB, please cite\001
     63+4 0 -1 0 0 18 12 0.0000 4 210 675 1425 1050 $close\001
     64+4 2 -1 0 0 18 12 0.0000 4 225 570 9450 1050 $help\001
     65+4 2 -1 0 0 18 12 0.0000 4 210 1140 9375 9990 $to:XY:box\001
     66+4 0 -1 0 0 18 12 0.0000 4 225 990 9150 10440 $Y:expert\001
     67+4 0 -1 0 0 18 12 0.0000 4 210 495 1500 5865 $box\001
     68+4 0 -1 0 0 18 12 0.0000 4 210 3690 1500 5340 Existing Files (f) and Directories (D)\001
     69+4 0 -1 0 0 18 12 0.0000 4 210 675 1620 10395 $Y:old\001
     70+4 0 -1 0 0 18 12 0.0000 4 210 660 4725 10388 $Y:del\001
     71+4 0 -1 0 0 18 12 0.0000 4 225 1500 1620 4725 $new_complex\001
     72+4 0 -1 0 0 18 12 0.0000 4 225 765 4455 4725 $merge\001
     73+4 1 -1 0 0 18 12 0.0000 4 165 915 7140 2865 Authors:\001
     74+4 1 -1 0 0 18 12 0.0000 4 225 585 5265 945 $logo\001
     75+4 1 -1 0 0 18 12 0.0000 4 210 2475 2745 3870 http://www.arb-home.de/\001
     76+4 1 -1 0 0 18 12 0.0000 4 210 2910 2745 3150 Department of Microbiology\001
     77+4 1 -1 0 0 18 10 0.0000 4 150 2295 2745 3375 Technical University of Munich\001
     78+4 1 -1 0 0 18 10 0.0000 4 150 675 2745 3555 Germany\001
     79+4 1 -1 0 0 18 11 0.0000 4 165 2340 7140 3345 Harald Meier, Yadhukumar\001
     80+4 1 -1 0 0 18 12 0.0000 4 210 4800 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001
     81+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
     82+4 1 -1 0 0 18 10 0.0000 4 150 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001
     83+4 1 -1 0 0 18 12 0.0000 4 210 900 5265 2610 $version\001
     84+4 0 -1 0 0 18 12 0.0000 4 210 2295 7350 10365 Y:Enable Expert Mode\001
     85+4 0 -1 0 0 18 10 0.0000 4 150 2190 1440 10800 Y:If you use ARB, please cite\001
     86+4 1 -1 0 0 18 10 0.0000 4 120 2085 7110 3960 Lead tester: F. O. Gloeckner\001
     87+4 1 -1 0 0 18 12 0.0000 4 225 1125 2745 2970 $copyright\001
     88+4 1 -1 0 0 18 12 0.0000 4 210 3600 7155 4185 Mac OS X port: Matthew T. Cottrell\001

  • Portfile

     
    44PortSystem              1.0
    55
    66name                    arb
    7 version                 5.1
    87epoch                   1
    9 revision                2
     8version                 5.2
    109categories              science
    1110maintainers             me.com:matt.cottrell
    1211platforms               darwin
    … …  
    2423                        (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment \
    2524                        for sequence data. Nucleic Acids Research. 32:1363-1371.
    2625
    27 fetch.type              svn
    28 svn.url                 http://svn.mikro.biologie.tu-muenchen.de/svn/branches/stable_5.0
    29 svn.revision            6215
    30 svn.method              checkout
    31 #fetch.user             coder             
    32 #fetch.password         gimmeARBsource
    33 #work around until ticket #21232 is resolved
    34 svn.args                --username coder --password gimmeARBsource
     26master_sites            http://download.arb-home.de/release/arb_${version}/
     27distname                arbsrc
     28extract.suffix          .tgz
     29dist_subdir             ${name}/${version}
     30worksrcdir              arbsrc_6779
    3531
     32checksums               sha1    4ee493a16ece5231d46ed1071407c06e733d67c8 \
     33                        rmd160  d9d99d0ebadaa293091ff93f6ca588b2321bd8b0
     34
     35depends_build           port:imake \
     36                        port:makedepend
     37
    3638depends_lib             port:openmotif \
    3739                        port:lynx \
    3840                        port:gsed \
    39                         port:imake \
    4041                        port:sablotron \
    4142                        port:mesa \
    4243                        port:glw \
    … …  
    5152                        patch-ARB-makefile.diff \
    5253                        patch-ARB-RNA3D_GlobalHeader.hxx.diff \
    5354                        patch-ARB-DARWIN.pl.diff \
    54                         patch-ARB-glpng.diff
     55                        patch-ARB-glpng.diff \
     56                        arb_intro.fig.diff
    5557                       
    56 worksrcdir              stable_5.0
    57 
    5858configure               {
    5959                        reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \
    6060                                                     ${worksrcpath}/util/arb_check_build_env.pl \
    … …  
    117117universal_variant       no
    118118
    119119post-activate           {
    120                         system "rm -rf `find ${prefix}/share/arb -type d -name .svn`"
    121                        
    122120                        # Provide users with copies of the default configuration and macros
    123121                        # if the user doesn't already have them.
    124122                        if {![file exists ${prefix}/share/arb/lib/arb_tcp.dat]} {
    … …  
    141139
    142140You have two options (A is easier, B is more difficult):
    143141
    144 A) Open a new terminal window and type arb_macsetup to set up your environment automatically
     142A) 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.
    145143
    146144or
    147145       
    148 B) Follow the steps below:
     146B) More difficult - follow the steps below:
    149147
    1501481)
    151149bash users add the following lines to your ~/.profile or to your ~/.bashrc
    … …  
    164162
    165163      enter the following command:
    166164      source ~/.cshrc
     1653)
     166create a text file in your home folder called .xmodmap that contains the text below:
     167
     168clear Mod1
     169clear Mod2
     170keycode 63 = Mode_switch
     171keycode 66 = Meta_L
     172keycode 69 = Meta_R
     173add Mod1 = Meta_L Meta_R
     174add Mod2 = Mode_switch
     175
    167176C)
     177to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup
     178
     179D)
    168180type arb to start ARB
    169181
    170182A demo data base is located at ${prefix}/share/arb/demo.arb