Ticket #28276: arb-5.2-ryandesign.diff

File arb-5.2-ryandesign.diff, 22.2 KB (added by ryandesign (Ryan Carsten Schmidt), 14 years ago)

proposed changes (incomplete)

  • files/patch-ARB-makefile.diff

     
    1 --- Makefile    (revision 6192)
    2 +++ Makefile    (working copy)
    3 @@ -202,11 +202,11 @@
     1--- Makefile.orig       2011-02-03 12:37:28.000000000 -0300
     2+++ Makefile    2011-02-04 17:05:56.000000000 -0300
     3@@ -31,11 +31,12 @@
     4 #                       configurable in config.makefile
     5 #
     6 # -----------------------------------------------------
     7+
     8 # Read configuration
     9 include config.makefile
     10 
     11 ifeq ($(LD_LIBRARY_PATH),'')
     12-LD_LIBRARY_PATH:=${ARBHOME}/lib
     13+       LD_LIBRARY_PATH:=${ARBHOME}/lib
     14 endif
     15 
     16 FORCEMASK = umask 002
     17@@ -46,8 +47,6 @@
     18 GPP:=g++
     19 CPPreal:=cpp
     20 
     21-
     22-
     23 # ---------------------- compiler version detection
     24 
     25 # supported compiler versions:
     26@@ -203,11 +202,12 @@
    427 XINCLUDES:=-I$(XHOME)/include
    528 
    629 ifdef DARWIN
    … …  
    1033 
    1134 ifdef DARWIN
    1235-       XLIBS := -L/usr/OpenMotif/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi
    13 +       XLIBS := -L$(PREFIX)/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi
     36+    #Explicit use of png12 because ARB breaks with png14 (http://www.libpng.org/pub/png/src/libpng-1.2.x-to-1.4.x-summary.txt)
     37+       XLIBS := -L$(PREFIX)/lib -lXm -lpng12 -lz -L$(XHOME)/lib -lXt -lX11 -lXext -lXp -lc -lXmu -lXi
    1438        XLIBS += -lGLU -lGL -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
    1539 else
    1640        XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXp -lXt -lXext -lX11
    17 @@ -225,14 +225,9 @@
     41@@ -226,14 +226,9 @@
    1842 
    1943 GL_PNGLIBS := -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng
    2044 
    … …  
    3256 GL_LIBS := $(GL_LIB) $(GLEWLIB) $(GLUTLIB) $(GL_PNGLIBS)
    3357 
    3458 #XLIBS += $(GL_LIB)
    35 @@ -247,11 +242,7 @@
     59@@ -248,11 +243,7 @@
    3660 
    3761 #---------------------- tiff lib:
    3862 
    … …  
    4569 
    4670 #---------------------- basic libs:
    4771 
    48 @@ -318,7 +309,7 @@
     72@@ -319,7 +310,7 @@
    4973 
    5074 CTAGS := etags
    5175 ifdef DARWIN
    … …  
    5377+       XMKMF := $(PREFIX)/bin/xmkmf
    5478 else
    5579        XMKMF := /usr/bin/X11/xmkmf
    56  endif
    57  No newline at end of file
     80 endif

  • 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:
    39 # The MacPorts PREFIX is typicaly /opt/local
    40 PREFIX=/opt/local
     39PREFIX=@@PREFIX@@
    4140BINPATH=${PREFIX}/bin
    4241SBINPATH=${PREFIX}/sbin
    4342MANPAGES=${PREFIX}/share/man
    4443TIMESTAMP=$(date +"%Y-%m-%d_at_%H:%M:%S")
    4544BACKUP_SUFFIX=macports-saved_${TIMESTAMP}
     45XMODMAP_FILE=xmodmap
    4646OUR_STRING="ARB Installer addition on ${TIMESTAMP}"
    4747
    4848# Determine the user's shell, in order to choose an appropriate configuration file we'll be tweaking.
    … …  
    105105    echo "An appropriate ${1} variable has been added to your shell environment by the ${3} installer."
    106106}
    107107
     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 "\n# ${OUR_STRING}: adding an appropriate ${1} variable for use with ${3}." >> ${HOME}/.${XMODMAP_FILE}
     119    echo "${1}\n ${2}\n ${3}\n ${4}\n ${5}\n ${6}\n ${7}\n" >> ${HOME}/.${XMODMAP_FILE}
     120    echo -e "# Finished adapting your xmodmap file for use with ARB.\n" >> ${HOME}/.${XMODMAP_FILE}
     121    chown ${USER} ${HOME}/.${XMODMAP_FILE} || echo "Warning: unable to adapt permissions on your ${HOME}/.${XMODMAP_FILE} shell configuration file!"
     122    echo "An appropriate xmodmap file has been added to your home folder by the ${8} installer."
     123}
     124
    108125# Confirm that MacPorts has been configured for this user:
    109126if ${SHELL} ${LOGIN_FLAG} -c "/usr/bin/printenv PATH" | grep ${PREFIX} > /dev/null; then
    110127    echo "Your shell already has the right PATH environment variable for use with MacPorts!"
    … …  
    149166        write_setting ARBHOME "${PREFIX}/share/arb" ARB
    150167fi
    151168
     169#write the .xmodmap file for easy keyboard shortcutsin the ARB sequence editor
     170write_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
     171
    152172# arb_setenv script is done with its job - exit gracefully!
    153173echo ""
    154174echo "You have succesfully installed ARB"

  • files/patch-ARB-config.makefile.diff

     
    55 PTPAN := 0
    66 
    77-ARB_64 := 0# compile 64bit ARB version
    8 +ARB_64 := 1# compile 64bit ARB version
     8+ARB_64 := @@64BIT@@# compile 64bit ARB version
    99 #BUILDHOST_64 := 1# whether build host is 64bit (value defaults to ARB_64). Needed for cross-compile
    1010 
    1111 # --------------------------------------------------------------------------------

  • 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
     8version                 5.2
    99categories              science
    1010maintainers             me.com:matt.cottrell
    1111platforms               darwin
    … …  
    1818                        nucleotide and amino acid sequences.  Features include routines for designing fluorescence in situ \
    1919                        hybridization (FISH) probes and PCR and sequencing primers.  Phylogenetic trees can be generated and \
    2020                        sequences can be added to existing trees.  ARB maintains links between the phylogenetic trees and sequences \
    21                         for data base search and query.  The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) \
    22                         maintaines up-to-date databases.  64-bit ARB is built on 10.6 in order to work with the largest data bases. \
    23                         32-bit ARB is built on 10.5.  An active community of scientists exchange tips on the ARB Yahoo! discussion group \
     21                        for database search and query.  The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) \
     22                        maintains up-to-date databases.  An active community of scientists exchanges tips on the ARB Yahoo! discussion group \
    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:gsed \
     36                        port:imake \
     37                        port:makedepend
     38
    3639depends_lib             port:openmotif \
    3740                        port:lynx \
    38                         port:gsed \
    39                         port:imake \
    4041                        port:sablotron \
    4142                        port:mesa \
    4243                        port:glw \
    4344                        port:glew \
    44                         port:tiff
     45                        port:tiff \
     46                        port:xfig \
     47                        port:gv
    4548
    4649patchfiles              patch-ARB-config.makefile.diff \
    4750                        patch-ARB-makefile.diff \
    4851                        patch-ARB-RNA3D_GlobalHeader.hxx.diff \
    49                         patch-ARB-DARWIN.pl.diff
     52                        patch-ARB-DARWIN.pl.diff \
     53                        arb_intro.fig.diff
    5054                       
    51 worksrcdir              stable_5.0
    52 
    53 use_configure           no
    5455configure.env           ARBHOME=${worksrcpath} 
    5556configure.env-append    PATH=${worksrcpath}/bin:$env(PATH)
    5657
    5758configure               {
    58                         reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL
    59                         reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu
    60                         reinplace "s| sed | gsed |g" ${worksrcpath}/util/arb_check_build_env.pl
    61                         reinplace "s| sed | gsed |g" ${worksrcpath}/arb_install.sh
    62                         reinplace "s| sed | gsed |g" ${worksrcpath}/WINDOW/AW_status.cxx
    63                         reinplace "s| sed | gsed |g" ${worksrcpath}/SH/example_batch_probe_match.sh
    64                         reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/GDEmenus
    65                         reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/genhelp.sh
    66                         reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/genhelptree.sh
    67                         reinplace "s| sed | gsed |g" ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh
    68                         reinplace "s| sed | gsed |g" ${worksrcpath}/HELP_SOURCE/Makefile
    69                         reinplace "s| sed | gsed |g" ${worksrcpath}/AISC_COM/AISC/Makefile
    70                         reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/Makefile
    71                         reinplace "s| sed | gsed |g" ${worksrcpath}/HELP_SOURCE/genhelp/Makefile
    72                         reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/Makefile.helpfiles
     59                        reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \
     60                                                     ${worksrcpath}/util/arb_check_build_env.pl \
     61                                                     ${worksrcpath}/arb_install.sh \
     62                                                     ${worksrcpath}/WINDOW/AW_status.cxx \
     63                                                     ${worksrcpath}/SH/example_batch_probe_match.sh \
     64                                                     ${worksrcpath}/GDEHELP/GDEmenus \
     65                                                     ${worksrcpath}/GDEHELP/genhelp.sh \
     66                                                     ${worksrcpath}/GDEHELP/genhelptree.sh \
     67                                                     ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh \
     68                                                     ${worksrcpath}/HELP_SOURCE/Makefile \
     69                                                     ${worksrcpath}/AISC_COM/AISC/Makefile \
     70                                                     ${worksrcpath}/GDEHELP/Makefile \
     71                                                     ${worksrcpath}/HELP_SOURCE/genhelp/Makefile \
     72                                                     ${worksrcpath}/GDEHELP/Makefile.helpfiles
    7373                        file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
    74                         reinplace "s|@@PREFIX@@|${prefix}|g" ${filespath}/arb_macsetup
    7574                        file copy ${filespath}/arb_macsetup ${worksrcpath}/bin
    76 }
     75                        reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL \
     76                                                             ${worksrcpath}/bin/arb_macsetup
    7777
    78 platform darwin 9      {
    79 post-configure         {
    80                        reinplace "s|ARB_64 := 1# compile 64bit ARB version|ARB_64 := 0# compile 64bit ARB version|g" ${worksrcpath}/config.makefile
     78                        reinplace "s|OSX_SDK:=/Developer/SDKs/MacOSX10.5.sdk|OSX_SDK:=${configure.sdkroot}|g" ${worksrcpath}/Makefile
     79
     80                        if {${build_arch} == "ppc" || ${build_arch} == "i386"} {
     81                            set is64bit 0
     82                        } else {
     83                            set is64bit 1
     84                        }
     85                        reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile
    8186}
    82 }
    8387
    84 build.env-append        ${configure.env}
    85 build.env-append        PREFIX=${prefix}
     88build.env-append        ${configure.env} \
     89                        PREFIX=${prefix}
     90build.args              GCC=${configure.cc} \
     91                        GPP=${configure.cxx} \
     92                        CPPreal=${configure.cpp}
    8693
    8794destroot.keepdirs       ${destroot}${prefix}/share/arb/lib/pts
    8895
    8996destroot                {
    9097                        eval xinstall -m 0755 [glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin
    91                         file mkdir ${destroot}${prefix}/share/arb
    9298                        file mkdir ${destroot}${prefix}/share/arb/bin
    9399                        file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib
    94100                        file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP
    … …  
    97103                        file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS
    98104                        file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH
    99105                        file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb
    100 }
    101 
    102 post-destroot           {
    103106                        system "chmod a+w ${destroot}${prefix}/share/arb/lib/arb_tcp.dat"
    104107                        system "chmod a+w ${destroot}${prefix}/share/arb/lib/pts"
    105108                        system "chmod a+w ${destroot}${prefix}/share/arb/lib/macros"
    106                         system "ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server"
    107                         system "ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server"
     109                        ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server
     110                        ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server
     111                        system "rm -rf `find ${destroot}${prefix}/share/arb -type d -name .svn`"
    108112}
    109                        
    110 post-activate           {
    111                         system "rm -rf `find ${prefix}/share/arb -type d -name .svn`"
    112113
    113 ui_msg "
     114universal_variant       no
     115
     116notes "
    114117****************************************************************
    115118Before running ARB you must set ARBHOME and add ARB to your PATH
    116119****************************************************************
    117120
    118121You have two options (A is easier, B is more difficult):
    119122
    120 A) Open a new terminal window and type arb_macsetup to set up your environment automatically
     123A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically.  This script also enables keyboard shortcuts used in the sequence editor.
    121124
    122125or
    123126       
    124 B) Follow the steps below:
     127B) More difficult - follow the steps below:
    125128
    126 1a)
     1291)
    127130bash users add the following lines to your ~/.profile or to your ~/.bashrc
    128131
    129132      ARBHOME=${prefix}/share/arb;export ARBHOME
    … …  
    132135
    133136      enter the following command:
    134137      . ~/.profile
    135 1b)
     1382)
    136139tcsh users add the following lines to your ~/.cshrc
    137140      setenv ARBHOME ${prefix}/share/arb
    138141      setenv PATH ${prefix}/share/arb\:\$PATH
    139142
    140143      enter the following command:
    141144      source ~/.cshrc
    142 2)
     1453)
     146create a text file in your home folder called .xmodmap that contains the text below:
     147
     148clear Mod1
     149clear Mod2
     150keycode 63 = Mode_switch
     151keycode 66 = Meta_L
     152keycode 69 = Meta_R
     153add Mod1 = Meta_L Meta_R
     154add Mod2 = Mode_switch
     155
     156C)
     157to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup
     158
     159D)
    143160type arb to start ARB
    144161
    145162A demo data base is located at ${prefix}/share/arb.demo.arb
    146163
    147164Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371
    148165"
    149 }
    150  No newline at end of file