SeqAn is an open source C++ library of efficient algorithms

and data structures for the analysis of sequences with the
focus on biological data. The library is licensed under the
3-clause BSD license except the applications which are GPL.

WWW: http://www.seqan.de/

PR:		167571
Submitted by:	Hannes <h2+fbsdports@fsfe.org>

biology/Makefile

@@ -85,6 +85,7 @@
     SUBDIR += recombine
     SUBDIR += ruby-bio
     SUBDIR += seaview
+    SUBDIR += seqan
     SUBDIR += seqio
     SUBDIR += sim4
     SUBDIR += ssaha

biology/seqan/Makefile

@@ -0,0 +1,49 @@
+# New ports collection makefile for:   seqan
+# Date created:        3 May 2012
+# Whom:                h2
+#
+# $FreeBSD$
+#
+
+PORTNAME=	seqan
+PORTVERSION=	1.3.1
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.seqan.de/releases/
+
+MAINTAINER=	h2+fsbdports@fsfe.org
+COMMENT=	C++ Sequence Analysis Library
+
+LICENSE=	BSD GPLv3
+LICENSE_COMB=	multi
+
+LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE
+LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE
+
+USE_ZIP=	yes
+
+USE_CMAKE=	yes
+CMAKE_SOURCE_PATH=${WRKSRC}/cmake
+CMAKE_OUTSOURCE=yes
+USE_PYTHON_BUILD=yes
+MAKE_JOB_SAFE=	yes
+
+SUB_FILES=	pkg-message
+PKG_MESSAGE=	${WRKDIR}/pkg-message
+
+.include <bsd.port.pre.mk>
+
+.if ${ARCH} == i386
+# triggers internal error in system gcc
+USE_GCC=	4.4+
+.endif
+
+# unsafe workaround because FreeBSD lacks logl and expl
+# see "BUGS" in `man 3 math`
+post-patch:
+	@${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h
+	@${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h
+
+post-install:
+	@${CAT} ${PKG_MESSAGE}
+
+.include <bsd.port.post.mk>

biology/seqan/distinfo

@@ -0,0 +1,2 @@
+SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
+SIZE (seqan-1.3.1.zip) = 8787521

biology/seqan/files/patch-cmake-CMakeLists.txt

@@ -0,0 +1,13 @@
+--- cmake/CMakeLists.txt.orig	2012-05-04 12:56:23.000000000 +0800
++++ cmake/CMakeLists.txt	2012-05-04 13:00:03.000000000 +0800
+@@ -146,6 +146,10 @@
+             COMPONENT headers)
+     #message("install(FILES ${HEADER} RENAME seqan${NEW_PATH} DESTINATION include COMPONENT headers)")
+ endforeach()
++#seqan.h
++install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../seqan.h
++	DESTINATION include
++	COMPONENT headers)
+ 
+ ################################################################################
+ # Set Compiler Flags

biology/seqan/files/patch-cmake-apps-CMakeLists.txt

@@ -0,0 +1,8 @@
+--- cmake/apps/CMakeLists.txt.orig	2012-05-04 11:12:35.000000000 +0800
++++ cmake/apps/CMakeLists.txt	2012-05-04 11:23:26.000000000 +0800
+@@ -108,4 +108,4 @@
+ 
+ # Install RazerS gapped parameters.
+ install(DIRECTORY ${SEQAN_LIBRARY}/apps/razers2/gapped_params
+-        DESTINATION bin)
++        DESTINATION share/seqan)

biology/seqan/files/pkg-message.in

@@ -0,0 +1,6 @@
+gapped_params for Razers2 have been installed to 
+      %%PREFIX%%/share/seqan/gapped_params
+      
+If you require these, make sure to set the correct 
+path with --param-dir as Razers2 will not pick them 
+up automatically.

biology/seqan/pkg-descr

@@ -0,0 +1,6 @@
+SeqAn is an open source C++ library of efficient algorithms
+and data structures for the analysis of sequences with the
+focus on biological data. The library is licensed under the
+3-clause BSD license except the applications which are GPL.
+
+WWW: http://www.seqan.de/