[153949] trunk/dports/science

[ryandesign at macports.org]

Revision: 153949
          https://trac.macports.org/changeset/153949
Author:   ryandesign at macports.org
Date:     2016-10-16 13:53:28 -0700 (Sun, 16 Oct 2016)
Log Message:
-----------
PEAR: New port, version 0.9.8

Resolves #51289

Added Paths:
-----------
    trunk/dports/science/PEAR/
    trunk/dports/science/PEAR/Portfile
    trunk/dports/science/PEAR/files/
    trunk/dports/science/PEAR/files/patch-configure.diff

Added: trunk/dports/science/PEAR/Portfile
===================================================================
--- trunk/dports/science/PEAR/Portfile	                        (rev 0)
+++ trunk/dports/science/PEAR/Portfile	2016-10-16 20:53:28 UTC (rev 153949)
@@ -0,0 +1,41 @@
+# -*- 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                PEAR
+version             0.9.8
+categories          science
+platforms           darwin
+license             CC-BY-NC-SA-3
+maintainers         yahoo.com:mashavecher
+
+description         PEAR - Paired-End reAd mergeR
+
+long_description    PEAR is an ultrafast, memory-efficient and highly \
+                    accurate pair-end read merger. It is fully parallelized \
+                    and can run with as low as just a few kilobytes of memory.
+
+homepage            http://www.exelixis-lab.org/web/software/pear
+master_sites        http://sco.h-its.org/exelixis/web/software/pear/files/
+distname            pear-${version}
+
+checksums           rmd160  c9703233b188527dcd281f6a2cc5f924a3a3828a \
+                    sha256  0fff7401d63141d9235aa28174113f346a039743c0c679b435f5230a32b28728
+
+depends_lib         port:bzip2 \
+                    port:zlib
+
+patchfiles          patch-configure.diff
+
+notes "
+The PEAR creative commons license prohibits commercial use of the code.\
+For testing and using PEAR on a commercial basis you need to purchase a\
+commercial software license.\
+If you wish to purchase such a license please contact:
+
+Prof. Alexandros Stamatakis <Alexandros.Stamatakis at h-its.org>
+
+Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
+Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593
+"


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

Added: trunk/dports/science/PEAR/files/patch-configure.diff
===================================================================
--- trunk/dports/science/PEAR/files/patch-configure.diff	                        (rev 0)
+++ trunk/dports/science/PEAR/files/patch-configure.diff	2016-10-16 20:53:28 UTC (rev 153949)
@@ -0,0 +1,12 @@
+./configure: line 2874: test: too many arguments
+--- configure.orig	2016-04-20 00:46:55.000000000 -0500
++++ configure	2016-05-07 21:38:05.000000000 -0500
+@@ -2871,7 +2871,7 @@
+ ac_config_headers="$ac_config_headers src/config.h"
+ 
+ 
+-if test -z $CFLAGS; then
++if test -z "$CFLAGS"; then
+     CFLAGS='-O3'
+ fi
+ 
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