[57345] trunk/dports/science
macsforever2000 at macports.org
macsforever2000 at macports.org
Wed Sep 9 21:29:26 PDT 2009
Revision: 57345
http://trac.macports.org/changeset/57345
Author: macsforever2000 at macports.org
Date: 2009-09-09 21:29:21 -0700 (Wed, 09 Sep 2009)
Log Message:
-----------
Added arb port. (#21155)
Added Paths:
-----------
trunk/dports/science/arb/
trunk/dports/science/arb/Portfile
trunk/dports/science/arb/files/
trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff
trunk/dports/science/arb/files/patch-ARB-RNA3D_GlobalHeader.hxx.diff
trunk/dports/science/arb/files/patch-ARB-config.makefile.diff
trunk/dports/science/arb/files/patch-ARB-makefile.diff
Added: trunk/dports/science/arb/Portfile
===================================================================
--- trunk/dports/science/arb/Portfile (rev 0)
+++ trunk/dports/science/arb/Portfile 2009-09-10 04:29:21 UTC (rev 57345)
@@ -0,0 +1,138 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem 1.0
+
+name arb
+version 5.19.0
+categories science
+maintainers me.com:matt.cottrell
+platforms darwin
+
+description ARB graphical DNA, RNA and amino acid sequence analysis tool
+
+homepage http://www.arb-home.de/
+
+long_description ARB is an application for genetic sequence analysis that includes tools for editing and aligning \
+ nucleotide and amino acid sequences. Features include routines for designing fluorescence in situ \
+ hybridization (FISH) probes and PCR and sequencing primers. Phylogenetic trees can be generated and \
+ sequences can be added to existing trees. ARB maintains links between the phylogenetic trees and sequences \
+ for data base search and query. The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) \
+ maintaines up-to-date databases. 64-bit ARB is built on 10.6 in order to work with the largest data bases. \
+ 32-bit ARB is built on 10.5. An active community of scientists exchange tips on the ARB Yahoo! discussion group \
+ (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 6192
+svn.method checkout
+#fetch.user coder
+#fetch.password gimmeARBsource
+#work around until ticket #21232 is resolved
+svn.args --username coder --password gimmeARBsource
+
+depends_lib port:openmotif \
+ port:lynx \
+ port:gsed \
+ port:imake \
+ port:sablotron \
+ port:mesa \
+ port:glw \
+ port:glew \
+ port:tiff
+
+patchfiles patch-ARB-config.makefile.diff \
+ patch-ARB-makefile.diff \
+ patch-ARB-RNA3D_GlobalHeader.hxx.diff \
+ patch-ARB-DARWIN.pl.diff
+
+worksrcdir stable_5.0
+
+use_configure no
+configure.env ARBHOME=${worksrcpath}
+configure.env-append PATH=${worksrcpath}/bin:$env(PATH)
+
+configure {
+ reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL
+ reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu
+ reinplace "s| sed | gsed |g" ${worksrcpath}/util/arb_check_build_env.pl
+ reinplace "s| sed | gsed |g" ${worksrcpath}/arb_install.sh
+ reinplace "s| sed | gsed |g" ${worksrcpath}/WINDOW/AW_status.cxx
+ reinplace "s| sed | gsed |g" ${worksrcpath}/SH/example_batch_probe_match.sh
+ reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/GDEmenus
+ reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/genhelp.sh
+ reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/genhelptree.sh
+ reinplace "s| sed | gsed |g" ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh
+ reinplace "s| sed | gsed |g" ${worksrcpath}/HELP_SOURCE/Makefile
+ reinplace "s| sed | gsed |g" ${worksrcpath}/AISC_COM/AISC/Makefile
+ reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/Makefile
+ reinplace "s| sed | gsed |g" ${worksrcpath}/HELP_SOURCE/genhelp/Makefile
+ reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/Makefile.helpfiles
+ file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
+}
+
+platform darwin 9 {
+post-configure {
+ reinplace "s|ARB_64 := 1# compile 64bit ARB version|ARB_64 := 0# compile 64bit ARB version|g" ${worksrcpath}/config.makefile
+}
+}
+
+build.env-append ${configure.env}
+build.env-append PREFIX=${prefix}
+
+destroot.keepdirs ${destroot}${prefix}/share/arb/lib/pts
+
+destroot {
+ eval xinstall -m 0755 [glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin
+ file mkdir ${destroot}${prefix}/share/arb
+ file mkdir ${destroot}${prefix}/share/arb/bin
+ file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib
+ file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP
+ file mkdir ${destroot}${prefix}/lib/help
+ file copy ${worksrcpath}/HELP_SOURCE/oldhelp ${destroot}${prefix}/lib/help
+ file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS
+ file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH
+ file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb
+}
+
+post-destroot {
+ system "chmod a+w ${destroot}${prefix}/share/arb/lib/arb_tcp.dat"
+ system "chmod a+w ${destroot}${prefix}/share/arb/lib/pts"
+ system "chmod a+w ${destroot}${prefix}/share/arb/lib/macros"
+ system "ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server"
+ system "ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server"
+}
+
+post-activate {
+ system "rm -rf `find ${prefix}/share/arb -type d -name .svn`"
+ui_msg "
+1)
+**************************************************************************
+bash-users add the following lines to your ~/.profile or to your ~/.bashrc
+**************************************************************************
+ ARBHOME=${prefix}/share/arb;export ARBHOME
+ PATH=${prefix}/share/arb/bin:\$PATH
+ export PATH
+
+ enter the following command:
+ . ~/.profile
+2)
+**************************************************
+tcsh users add the following lines to your ~/.cshrc
+**************************************************
+ setenv ARBHOME ${prefix}/share/arb
+ setenv PATH ${prefix}/share/arb\:\$PATH
+
+ enter the following command:
+ source ~/.cshrc
+3)
+*********************
+type arb to start ARB
+*********************
+
+A demo data base is located at ${prefix}/share/arb.demo.arb
+
+Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371
+"
+}
\ No newline at end of file
Property changes on: trunk/dports/science/arb/Portfile
___________________________________________________________________
Added: svn:keywords
+ Id
Added: svn:eol-style
+ native
Added: trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff 2009-09-10 04:29:21 UTC (rev 57345)
@@ -0,0 +1,12 @@
+--- PERL2ARB/DARWIN.PL (revision 6192)
++++ PERL2ARB/DARWIN.PL (working copy)
+@@ -4,8 +4,7 @@
+ WriteMakefile(
+ 'NAME' => 'ARB',
+ 'VERSION_FROM' => 'ARB.pm', # finds $VERSION
+- #'LIBS' => '-L../ARBDB2 -lARBDB -L/usr/local/lib/perl5/5.10.0/darwin-2level/CORE/ -lperl', # e.g., '-lm'
+- 'LIBS' => '-L../ARBDB2 -lARBDB -L/System/Library/Perl/lib/5.10/ -lperl', #System provides 64-bit Perl with Snow Leopard
++ 'LIBS' => '-L../ARBDB2 -lARBDB -L@@PREFIX@@/lib/perl5/5.8.9/darwin-2level/CORE/ -lperl', #MacPorts installs 64-bit perl5.8.9
+ 'DEFINE' => '', # e.g., '-DHAVE_SOMETHING'
+ 'INC' => '-I../INCLUDE', # e.g., '-I/usr/include/other'
+ 'CCFLAGS' => '-arch x86_64',
Added: trunk/dports/science/arb/files/patch-ARB-RNA3D_GlobalHeader.hxx.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-RNA3D_GlobalHeader.hxx.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-RNA3D_GlobalHeader.hxx.diff 2009-09-10 04:29:21 UTC (rev 57345)
@@ -0,0 +1,14 @@
+--- RNA3D/RNA3D_GlobalHeader.hxx (revision 6192)
++++ RNA3D/RNA3D_GlobalHeader.hxx (working copy)
+@@ -31,7 +31,11 @@
+ // working on ralfs machine
+ // working on waltz too
+ #include <GL/glew.h>
++#ifdef DARWIN
++#include <glut.h>
++#else
+ #include <GL/glut.h>
++#endif
+ #include <GL/glpng.h>
+
+ // @@@ HACK @@@
\ No newline at end of file
Added: trunk/dports/science/arb/files/patch-ARB-config.makefile.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-config.makefile.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-config.makefile.diff 2009-09-10 04:29:21 UTC (rev 57345)
@@ -0,0 +1,32 @@
+--- config.makefile 2009-09-05 20:38:12.000000000 -0400
++++ config.makefile.template 2009-09-05 20:42:44.000000000 -0400
+@@ -20,7 +20,7 @@
+ # 2 = compile both, use old (recommended for development only)
+ PTPAN := 0
+
+-ARB_64 := 0# compile 64bit ARB version
++ARB_64 := 1# compile 64bit ARB version
+ #BUILDHOST_64 := 1# whether build host is 64bit (value defaults to ARB_64). Needed for cross-compile
+
+ # --------------------------------------------------------------------------------
+@@ -30,8 +30,8 @@
+ # ------------
+ # Section: Linux
+
+-MACH := LINUX# Linux g++ and gcc
+-LINUX := 1
++#MACH := LINUX# Linux g++ and gcc
++#LINUX := 1
+
+ # DEBIAN := 1 # uncomment for DEBIAN systems
+ # REDHAT := 1 # uncomment for REDHAT systems
+@@ -39,7 +39,7 @@
+ # ------------
+ # Section: Mac OSX
+
+-# MACH := DARWIN#
+-# DARWIN := 1
++ MACH := DARWIN#
++ DARWIN := 1
+
+ # ------------
Added: trunk/dports/science/arb/files/patch-ARB-makefile.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-makefile.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-makefile.diff 2009-09-10 04:29:21 UTC (rev 57345)
@@ -0,0 +1,56 @@
+--- Makefile (revision 6192)
++++ Makefile (working copy)
+@@ -202,11 +202,11 @@
+ XINCLUDES:=-I$(XHOME)/include
+
+ ifdef DARWIN
+- XINCLUDES := -I/sw/include -I$(OSX_SDK)/usr/X11/include -I$(OSX_SDK)/usr/include/krb5 -I/usr/OpenMotif/include #Snow Leopard couldn't find OpenMotif
++ XINCLUDES := -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/X11/include -I$(OSX_SDK)/usr/include/krb5 -I$(OSX_FW)/GLUT.framework/Headers -I$(PREFIX)/include
+ endif
+
+ ifdef DARWIN
+- XLIBS := -L/usr/OpenMotif/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi
++ XLIBS := -L$(PREFIX)/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi
+ XLIBS += -lGLU -lGL -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
+ else
+ XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXp -lXt -lXext -lX11
+@@ -225,14 +225,9 @@
+
+ GL_PNGLIBS := -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng
+
+- ifdef DARWIN
+- GLEWLIB := -L/usr/lib -lGLEW -L$(OSX_SDK)/usr/X11/lib -lGLw
+- GLUTLIB := -L$(XHOME)/lib -lglut
+- else
+- GLEWLIB := -lGLEW -lGLw
+- GLUTLIB := -lglut
+- endif
+-
++GLEWLIB := -lGLEW -lGLw
++GLUTLIB := -lglut
++
+ GL_LIBS := $(GL_LIB) $(GLEWLIB) $(GLUTLIB) $(GL_PNGLIBS)
+
+ #XLIBS += $(GL_LIB)
+@@ -247,11 +242,7 @@
+
+ #---------------------- tiff lib:
+
+-ifdef DARWIN
+- TIFFLIBS := -L/usr/local/lib -ltiff -L$(OSX_FW_IMAGEIO) -lTIFF
+-else
+- TIFFLIBS := -ltiff
+-endif
++TIFFLIBS := -ltiff
+
+ #---------------------- basic libs:
+
+@@ -318,7 +309,7 @@
+
+ CTAGS := etags
+ ifdef DARWIN
+- XMKMF := /usr/X11/bin/xmkmf
++ XMKMF := $(PREFIX)/bin/xmkmf
+ else
+ XMKMF := /usr/bin/X11/xmkmf
+ endif
\ No newline at end of file
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