[100324] trunk/dports/math

[ryandesign at macports.org]

Revision: 100324
          https://trac.macports.org/changeset/100324
Author:   ryandesign at macports.org
Date:     2012-12-08 02:39:19 -0800 (Sat, 08 Dec 2012)
Log Message:
-----------
prc: new port, version 1.5.6 (#37182)

Added Paths:
-----------
    trunk/dports/math/prc/
    trunk/dports/math/prc/Portfile
    trunk/dports/math/prc/files/
    trunk/dports/math/prc/files/patch-Makefile.in.diff
    trunk/dports/math/prc/files/patch-configure.diff

Added: trunk/dports/math/prc/Portfile
===================================================================
--- trunk/dports/math/prc/Portfile	                        (rev 0)
+++ trunk/dports/math/prc/Portfile	2012-12-08 10:39:19 UTC (rev 100324)
@@ -0,0 +1,57 @@
+# -*- 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                prc
+version             1.5.6
+categories          math science
+platforms           darwin
+maintainers         ryandesign openmaintainer
+license             GPL-2+
+
+description         program for aligning and scoring two profile hidden \
+                    Markov models
+
+long_description    PRC is a stand-alone program for aligning and scoring two \
+                    profile hidden Markov models. This can be used to detect \
+                    remote relationships between profiles more effectively \
+                    than by doing simple profile-sequence comparisons. \
+                    PRC takes into account all transition and emission \
+                    probabilities in both hidden Markov models. \
+                    PRC can read SAM, HMMER, PSI-BLAST and FASTA files.
+
+homepage            http://supfam.mrc-lmb.cam.ac.uk/PRC/
+master_sites        ${homepage}programs/PRC-${version}
+
+extract.suffix      .tgz
+distfiles           ${name}-${version}-src${extract.suffix}
+
+checksums           rmd160  1a79a72cf7329a6cb4433d2cf67c4ce123f1b605 \
+                    sha256  2ad9dcd0621a7262b5754426a62cd630dfbf14b04481fde116fa169d89249394
+
+patchfiles          patch-configure.diff \
+                    patch-Makefile.in.diff
+
+destroot {
+    xinstall -W ${worksrcpath} \
+        convert_to_prc \
+        merge_aligns.pl \
+        prc \
+        ${destroot}${prefix}/bin
+    
+    set docdir ${prefix}/share/doc/${name}
+    xinstall -d ${destroot}${docdir}
+    xinstall -W ${worksrcpath} -m 644 \
+        COPYING \
+        LICENSE \
+        README \
+        ${destroot}${docdir}
+    
+    xinstall -d ${destroot}${prefix}/share/examples
+    copy ${worksrcpath}/example ${destroot}${prefix}/share/examples/${name}
+}
+
+livecheck.type      regex
+livecheck.url       ${homepage}programs/
+livecheck.regex     PRC-(\[0-9.\]+)/


Property changes on: trunk/dports/math/prc/Portfile
___________________________________________________________________
Added: svn:keywords
   + Id
Added: svn:eol-style
   + native

Added: trunk/dports/math/prc/files/patch-Makefile.in.diff
===================================================================
--- trunk/dports/math/prc/files/patch-Makefile.in.diff	                        (rev 0)
+++ trunk/dports/math/prc/files/patch-Makefile.in.diff	2012-12-08 10:39:19 UTC (rev 100324)
@@ -0,0 +1,11 @@
+--- Makefile.in.orig	2009-07-07 14:58:30.000000000 -0500
++++ Makefile.in	2012-12-02 03:37:37.000000000 -0600
+@@ -6,7 +6,7 @@
+           -DPROF_HMM_TRANS=PLAN9      \
+           -DPAIR_HMM_STATES=SPACE5    \
+           -DPAIR_HMM_TRANS=ALL_TRANS
+-LIBS    = @LIBS@
++LIBS    = @LIBS@ @LDFLAGS@
+ 
+ 
+ # assorted variables

Added: trunk/dports/math/prc/files/patch-configure.diff
===================================================================
--- trunk/dports/math/prc/files/patch-configure.diff	                        (rev 0)
+++ trunk/dports/math/prc/files/patch-configure.diff	2012-12-08 10:39:19 UTC (rev 100324)
@@ -0,0 +1,10 @@
+--- configure.orig	2009-07-07 12:04:33.000000000 -0500
++++ configure	2012-12-02 03:29:19.000000000 -0600
+@@ -1357,7 +1357,6 @@
+                ;;
+     esac
+ else
+-    CFLAGS="-O3 -Wall -Werror"
+     case "${host}" in
+           alpha* )
+ 	       CFLAGS="${CFLAGS} -mieee"
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