added science apps

science/Portfile

@@ -0,0 +1,45 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; truncate-lines: t; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:et:sw=4:ts=4:sts=4
+# $Id: Portfile 73515 2010-11-16 09:04:19Z jmr@macports.org $
+
+PortSystem          1.0
+
+name                tokyocabinet-java
+version             1.18
+categories          databases java
+maintainers         ieure
+description         Java API for Tokyo Cabinet, a modern DBM
+long_description    Clojure is a dynamic programming language for the JVM.
+
+homepage            http://tokyocabinet.sourceforge.net/
+platforms           darwin
+depends_build       port:tokyocabinet
+master_sites        sourceforge:tokyocabinet
+
+checksums           md5 b87d892620df55e1088b6b8e22d87ad5 \
+                    sha1 d7e98944fbdc0753477c0d430a056de2fac07695 \
+                    rmd160 f354be0d0929860062812278f5f178aae64d2a36
+
+set javahome        /System/Library/Frameworks/JavaVM.framework
+
+
+## patch ##
+patch.args          -p1
+patchfiles          patch-Makefile.in.diff
+
+## configure ##
+configure.env       MYJAVAHOME=${javahome} \
+                    CFLAGS="-I${prefix}/include -I${javahome}/Headers" \
+                    LDFLAGS=-L${prefix}/lib INCLUDEDIR=${javahome}/Headers
+
+## build ##
+build.env           CFLAGS="-I${prefix}/include -I${javahome}/Headers" \
+                    LDFLAGS=-L${prefix}/lib
+
+post-destroot {
+    set jarfile tokyocabinet.jar
+    set javadir ${destroot}${prefix}/share/java
+    set dest    ${javadir}/${jarfile}
+
+    xinstall -m 0755 -d ${javadir}
+    file rename ${destroot}${prefix}/lib/${jarfile} ${dest}
+}

science/cndtools/Portfile

@@ -0,0 +1,20 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; truncate-lines: t; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem          1.0
+
+name                cndtools
+version             2010.10.11
+categories          science
+maintainers         bioperl.org:jason
+description         cndtools are Colin Dewey's tools including Mercator and Parametric alignments
+long_description    cndtools are Colin Dewey's tools including Mercator and Parametric alignments
+
+homepage            http://www.biostat.wisc.edu/~cdewey/software.html
+platforms           darwin
+master_sites        http://www.biostat.wisc.edu/~cdewey/software/cndsrc-2010.10.11.tar.gz
+
+checksums           md5 71e369f6891e7f33ff7331b14c972dd0 \
+                    sha1 1162d395524c2ed1615966b0728c9b68588f1723 \
+                    rmd160 60520905a68cb1b369757719b931d212137dc837
+

science/fsa/Portfile

@@ -0,0 +1,27 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; truncate-lines: t; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem          1.0
+
+name                fsa
+version             1.15.6
+categories          science
+maintainers         bioperl.org:jason
+description         FSA is a probabilistic multiple sequence alignment algorithm
+long_description    FSA is a probabilistic multiple sequence alignment algorithm which \
+uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
+
+
+homepage            http://fsa.sourceforge.net/
+platforms           darwin
+depends_build       port:exonerate port:mummer
+master_sites        sourceforge:fsa
+
+checksums           md5 9efd710f7bdff8319b32c4636edfbb45 \
+                    sha1 305a99a1f85acc83ddd687206d1e5816a709a779 \
+                    rmd160 1b6e9ebf848023a4a0e13421860a3b3b9a026202
+
+
+configure.args      --with-mummer yes \
+                    --with-exonerate yes \
+                    --enable-intel64

science/fsa/work

@@ -0,0 +1 @@
+/opt/local/var/macports/build/_Users_jstajich_macports_science_fsa/work

science/mummer/Portfile

@@ -0,0 +1,19 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; truncate-lines: t; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem          1.0
+
+name                mummer
+version             3.22
+categories          science
+maintainers         bioperl.org:jason
+description         MUMmer is a system for rapidly aligning entire genome
+long_description    MUMmer is a system for rapidly aligning entire genome using suffix trees.
+
+homepage            http://mummer.sourceforge.net/
+platforms           darwin
+master_sites        sourceforge:mummer
+
+checksums           md5 2cda5e6852828913d4a0af9f0fe9e9d8 \
+                    sha1 c763649fa12b3bdf4598bde4f292f9460bf2d47c \
+                    rmd160 f3c20f8458318dcf3251fb68bfd54c9513bf09ae

science/mummer/work

@@ -0,0 +1 @@
+/opt/local/var/macports/build/_Users_jstajich_macports_science_mummer/work