[76582] trunk/dports/science/arb
ryandesign at macports.org
ryandesign at macports.org
Mon Feb 28 13:16:11 PST 2011
Revision: 76582
http://trac.macports.org/changeset/76582
Author: ryandesign at 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"
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