source: trunk/dports/science/arb/Portfile

Last change on this file was 148323, checked in by khindenburg@…, 15 months ago

elixir, arb: add conflicts to each other (bin/mix)

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 9.1 KB
Line 
1# -*- 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
2# $Id: Portfile 148323 2016-05-04 02:28:50Z ryandesign@macports.org $
3
4PortSystem              1.0
5PortGroup               compiler_blacklist_versions 1.0
6
7name                    arb
8epoch                   2
9version                 6.0.4
10categories              science
11maintainers             mac.com:matt.cottrell
12platforms               darwin
13
14description             ARB graphical DNA, RNA and amino acid sequence analysis tool
15
16homepage                http://www.arb-home.de/
17
18long_description        ARB is an application for genetic sequence analysis that includes tools for editing and aligning \
19                        nucleotide and amino acid sequences.  Features include routines for designing fluorescence in situ \
20                        hybridization (FISH) probes and PCR and sequencing primers.  Phylogenetic trees can be generated and \
21                        sequences can be added to existing trees.  ARB maintains links between the phylogenetic trees and sequences \
22                        for database search and query.  The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) \
23                        maintains up-to-date databases.  An active community of scientists exchanges tips on the ARB Yahoo! discussion group \
24                        (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment \
25                        for sequence data. Nucleic Acids Research. 32:1363-1371.
26
27license                 Restrictive/Distributable
28
29master_sites            http://download.arb-home.de/release/${name}-${version}/
30distname                arb-${version}-source
31extract.suffix          .tgz
32worksrcdir              arbsrc_14797
33
34checksums               rmd160  a7e6ba2dff3eceba97d17e076c3efb333930dd72 \
35                        sha256  875301f138974694144b11091b0303a22efcfe7c6291c438881da64179820ce0
36
37# bin/mix
38conflicts               elixir
39
40depends_build           port:makedepend \
41                        port:pkgconfig
42
43depends_lib             port:openmotif \
44                        port:lynx \
45                        port:gsed \
46                        port:sablotron \
47                        port:glw \
48                        port:glew \
49                        port:xfig \
50                        port:gv \
51                        port:xorg-libXaw \
52                        port:gtime \
53                        path:lib/pkgconfig/glib-2.0.pc:glib2 \
54                        port:coreutils
55
56patchfiles              patch-ARB-config.makefile.diff \
57                        patch-ARB-intro.fig.diff \
58                        patch-ARB-arb.diff
59                       
60platform darwin {
61    if {${os.major} < 11} {
62        depends_build-append port:coreutils
63
64        configure.env-append INSTALL=${prefix}/bin/ginstall
65    }
66}
67                       
68# https://trac.macports.org/ticket/44368
69platform darwin 11 {
70    pre-patch {
71        # DOS to UNIX line endings so we can patch.
72        reinplace "s|\r||g" ${worksrcpath}/GDE/MUSCLE/src/globalsosx.cpp
73    }
74
75    patchfiles-append   patch-ARB-globalsosx.cpp.diff
76}
77
78configure               {
79                        if {${build_arch} eq "ppc" || ${build_arch} eq "i386"} {
80                            set is64bit 0
81                        } else {
82                            set is64bit 1
83                        }
84
85                        file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
86                        reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile
87                        reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/SH/arb_macsetup
88}
89
90build.env-append        PREFIX=${prefix} \
91                        ARBHOME=${worksrcpath} \
92                        PATH=${worksrcpath}/bin:$env(PATH)
93
94compiler.blacklist      *gcc-4.0 *gcc-4.2 {clang < 138}
95
96build.args-append       CXX=${configure.cxx} \
97                        CC=${configure.cc}
98
99destroot.keepdirs       ${destroot}${prefix}/share/arb/lib/pts
100
101destroot                {
102                        # Give the default settings a recognizable name ending in .default
103                        file rename ${worksrcpath}/lib/arb_tcp.dat ${worksrcpath}/lib/arb_tcp.dat.default
104                        file rename ${worksrcpath}/lib/macros ${worksrcpath}/lib/macros.default
105
106                        xinstall -m 0755 {*}[glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin
107
108                        file mkdir ${destroot}${prefix}/share/arb/bin
109                        file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS
110                        file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP
111                        file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib
112                        file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH
113                        file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb
114
115                        file mkdir ${destroot}${prefix}/lib/help
116                        file copy ${worksrcpath}/HELP_SOURCE/oldhelp ${destroot}${prefix}/lib/help
117
118                        ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server
119                        ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server
120                        ln -s ${prefix}/bin/muscle ${destroot}${prefix}/share/arb/bin/muscle
121
122                        xinstall -m 777 -d ${destroot}${prefix}/share/arb/lib/pts
123}
124
125# to be investigated later
126universal_variant       no
127
128post-activate           {
129                        # Provide users with copies of the default configuration and macros
130                        # if the user doesn't already have them.
131                        if {![file exists ${prefix}/share/arb/lib/arb_tcp.dat]} {
132                            xinstall -m 777 ${prefix}/share/arb/lib/arb_tcp.dat.default \
133                                ${prefix}/share/arb/lib/arb_tcp.dat
134                        }
135                        if {![file exists ${prefix}/share/arb/lib/macros]} {
136                            file copy ${prefix}/share/arb/lib/macros.default \
137                                ${prefix}/share/arb/lib/macros
138                            fs-traverse item ${prefix}/share/arb/lib/macros {
139                                file attributes ${item} -permissions a+w
140                            }
141                        }
142}
143
144notes "
145****************************************************************
146Before running ARB you must set ARBHOME and add ARB to your PATH
147****************************************************************
148
149You have two options (A is easier, B is more difficult):
150
151A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically.  This script also enables keyboard shortcuts used in the sequence editor.
152
153or
154       
155B) More difficult - follow the steps below:
156
1571)
158bash users add the following lines to your ~/.profile or to your ~/.bashrc
159
160      ARBHOME=${prefix}/share/arb;export ARBHOME
161      PATH=${prefix}/share/arb/bin:\$PATH
162      export PATH
163
164      enter the following command:
165      . ~/.profile
1662)
167tcsh users add the following lines to your ~/.cshrc
168     
169      setenv ARBHOME ${prefix}/share/arb
170      setenv PATH ${prefix}/share/arb\:\$PATH
171
172      enter the following command:
173      source ~/.cshrc
174
175C) to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup
176
177************************************************************************************************************************************
178You can set up keyboard shortcuts manually by creating a text file in your home folder called .xmodmap that contains the text below:
179************************************************************************************************************************************
180
181clear Mod1
182clear Mod2
183keycode 63 = Mode_switch
184keycode 66 = Meta_L
185keycode 69 = Meta_R
186add Mod1 = Meta_L Meta_R
187add Mod2 = Mode_switch
188
189*******************************************************************
190Use keys Control+Command Arrow Key to jump over bases
191Use Keys Option Arrow Key to pull in bases across alignment gaps
192Use the right Command Key plus a letter key to activate a menu item
193*******************************************************************
194
195*****************************
196Type 'arb' to start using ARB
197*****************************
198
199A demo data base is located at ${prefix}/share/arb/demo.arb
200
201User generated macros, arb_tcp.dat and pt_servers have been preserved,
202but you should keep backups of these just in case.  They are located at:
203
204${prefix}/share/arb/lib/macros/
205${prefix}/share/arb/lib/arb_tcp.dat
206${prefix}/share/arb/lib/pts/
207
208Default settings are maintained at:
209
210${prefix}/share/arb/lib/macros.default/
211${prefix}/share/arb/lib/arb_tcp.dat.default
212
213These notes can be viewed at any time by typing 'port notes arb'
214
215Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371
216"
217
218livecheck.type          regex
219livecheck.url           http://download.arb-home.de/build/
220livecheck.regex         ${name}-(\[0-9.\]+)
Note: See TracBrowser for help on using the repository browser.