New port: biology/seqan-apps

SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.

This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged seperately and the library
can be found at biology/seqan.

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

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>

5 files changed, 220 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 97cdac5ece8c..4a21bff385f4 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -90,6 +90,7 @@
     SUBDIR += samtools
     SUBDIR += seaview
     SUBDIR += seqan
+    SUBDIR += seqan-apps
     SUBDIR += seqio
     SUBDIR += seqtools
     SUBDIR += sim4
diff --git a/biology/seqan-apps/Makefile b/biology/seqan-apps/Makefile
new file mode 100644
index 000000000000..e5ed8f45e71c
--- /dev/null
+++ b/biology/seqan-apps/Makefile
@@ -0,0 +1,46 @@
+# Created by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
+# $FreeBSD$
+
+PORTNAME=	seqan-apps
+PORTVERSION=	2.1.1
+DISTVERSIONPREFIX=	seqan-v
+CATEGORIES=	biology
+
+MAINTAINER=	h2+fbsdports@fsfe.org
+COMMENT=	Official Bioinformatic applications based on the SeqAn library
+
+LICENSE=	BSD3CLAUSE LGPL3 GPLv3
+LICENSE_COMB=	multi
+
+BUILD_DEPENDS=	boost-libs>0:devel/boost-libs
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	seqan
+GH_PROJECT=	seqan
+
+# once #199603 is resolved, do the following instead of USE_GCC
+# USES=		cmake:outsource compiler:openmp,c++14-lang
+USES=		cmake:outsource
+CMAKE_ARGS=	-DSEQAN_BUILD_SYSTEM="SEQAN_RELEASE_APPS"
+
+USE_GCC=	4.9+
+
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 1000000
+post-patch:
+	# missing C99 functions in FreeBSD's math.h, use C++ instead
+	@${REINPLACE_CMD} -e 's|expl(|std::exp(|g' ${WRKSRC}/apps/snp_store/snp_store.h
+	@${REINPLACE_CMD} -e 's|logl(|std::log(|g' ${WRKSRC}/apps/snp_store/snp_store.h
+	# the other way around (use math.h instead of cmath)
+	@${REINPLACE_CMD} -e 's|std::round|round|g' ${WRKSRC}/apps/yara/mapper_writer.h
+	@${REINPLACE_CMD} -e 's|std::erfc|erfc|g' ${WRKSRC}/apps/yara/bits_matches.h
+.endif
+
+.if ${ARCH} == "i386"
+PLIST_SUB+=	RM_I386="@comment "
+.else
+PLIST_SUB+=	RM_I386=""
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/seqan-apps/distinfo b/biology/seqan-apps/distinfo
new file mode 100644
index 000000000000..8d2727d8717b
--- /dev/null
+++ b/biology/seqan-apps/distinfo
@@ -0,0 +1,2 @@
+SHA256 (seqan-seqan-seqan-v2.1.1_GH0.tar.gz) = df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c
+SIZE (seqan-seqan-seqan-v2.1.1_GH0.tar.gz) = 110874831
diff --git a/biology/seqan-apps/pkg-descr b/biology/seqan-apps/pkg-descr
new file mode 100644
index 000000000000..fbcdf62521e2
--- /dev/null
+++ b/biology/seqan-apps/pkg-descr
@@ -0,0 +1,11 @@
+SeqAn is an open source C++ library of efficient algorithms
+and data structures for the analysis of sequences with the
+focus on biological data. 
+
+This port contains applications built on SeqAn and developed
+within the SeqAn project. Among them are famous read mappers
+like RazerS and Yara, as well as many other tools. Some
+applications are packaged seperately and the library
+can be found at biology/seqan.
+
+WWW: http://www.seqan.de/
diff --git a/biology/seqan-apps/pkg-plist b/biology/seqan-apps/pkg-plist
new file mode 100644
index 000000000000..747936672f94
--- /dev/null
+++ b/biology/seqan-apps/pkg-plist
@@ -0,0 +1,160 @@
+bin/alf
+bin/bam2roi
+bin/bed_sort.sh
+bin/bisar
+bin/casbar
+%%RM_I386%%bin/compute_gain
+bin/dfi
+%%RM_I386%%bin/fiona
+bin/four2three
+bin/fx_bam_coverage
+bin/gff_sort.sh
+bin/gustaf
+bin/gustaf_mate_joining
+bin/insegt
+bin/mason_frag_sequencing
+bin/mason_genome
+bin/mason_materializer
+bin/mason_methylation
+bin/mason_simulator
+bin/mason_splicing
+bin/mason_variator
+bin/micro_razers
+bin/pair_align
+bin/param_chooser
+bin/plot.awk
+bin/ps2pswLinks.gawk
+bin/rabema_build_gold_standard
+bin/rabema_evaluate
+bin/rabema_prepare_sam
+bin/razers
+bin/razers3
+bin/rep_sep
+bin/roi_feature_projection
+bin/roi_plot_9.sh
+bin/roi_plot_thumbnails
+bin/roi_sort.sh
+bin/s4_join
+bin/s4_search
+bin/sak
+bin/sam2matrix
+bin/samcat
+bin/seqan_tcoffee
+bin/seqcons2
+bin/sgip
+bin/snp_store
+%%RM_I386%%bin/splazers
+bin/stellar
+bin/tree_recon
+bin/yara_indexer
+bin/yara_mapper
+share/doc/alf/LICENSE
+share/doc/alf/README
+share/doc/alf/example/small.fasta
+share/doc/bs_tools/LICENSE
+share/doc/bs_tools/README
+share/doc/dfi/LICENSE
+share/doc/dfi/README
+share/doc/dfi/example/fasta1.fa
+share/doc/dfi/example/fasta2.fa
+%%RM_I386%%share/doc/fiona/LICENSE
+%%RM_I386%%share/doc/fiona/README
+%%RM_I386%%share/doc/fiona/example/reads.fa
+share/doc/fx_tools/LICENSE
+share/doc/fx_tools/README
+share/doc/gustaf/LICENSE
+share/doc/gustaf/README
+share/doc/gustaf/example/adeno.fa
+share/doc/gustaf/example/adeno_modified.fa
+share/doc/gustaf/example/adeno_modified_reads.fa
+share/doc/gustaf/example/stellar.gff
+share/doc/insegt/LICENSE
+share/doc/insegt/README
+share/doc/insegt/example/annoOutput.gff
+share/doc/insegt/example/annotations.gff
+share/doc/insegt/example/readOutput.gff
+share/doc/insegt/example/tupleOutput.gff
+share/doc/mason2/LICENSE
+share/doc/mason2/README
+share/doc/mason2/README.mason_frag_sequencing
+share/doc/mason2/README.mason_genome
+share/doc/mason2/README.mason_materializer
+share/doc/mason2/README.mason_methylation
+share/doc/mason2/README.mason_simulator
+share/doc/mason2/README.mason_splicing
+share/doc/mason2/README.mason_variator
+share/doc/mason2/example/adeno_virus.fa
+share/doc/micro_razers/LICENSE
+share/doc/micro_razers/README
+share/doc/micro_razers/example/genome.fa
+share/doc/micro_razers/example/reads.fa
+share/doc/micro_razers/example/reads.fa.result
+share/doc/ngs_roi/LICENSE
+share/doc/ngs_roi/R/ngsroi_0.1.tar.gz
+share/doc/ngs_roi/R/ngsroi_0.1.zip
+share/doc/ngs_roi/README
+share/doc/ngs_roi/example/dmel.bed
+share/doc/ngs_roi/example/dmel.gtf
+share/doc/ngs_roi/example/example.bam
+share/doc/pair_align/LICENSE
+share/doc/pair_align/README
+share/doc/param_chooser/LICENSE
+share/doc/param_chooser/README
+share/doc/rabema/LICENSE
+share/doc/rabema/README
+share/doc/razers/LICENSE
+share/doc/razers/README
+share/doc/razers/example/genome.fa
+share/doc/razers/example/reads.fa
+share/doc/razers/example/reads2.fa
+share/doc/razers3/LICENSE
+share/doc/razers3/README
+share/doc/razers3/example/genome.fa
+share/doc/razers3/example/reads.fa
+share/doc/razers3/example/reads2.fa
+share/doc/rep_sep/LICENSE
+share/doc/rep_sep/README
+share/doc/sak/LICENSE
+share/doc/sak/README
+share/doc/sak/README.sak.txt
+share/doc/sak/man/sak.1
+share/doc/sam2matrix/LICENSE
+share/doc/sam2matrix/README
+share/doc/samcat/LICENSE
+share/doc/samcat/README
+share/doc/searchjoin/LICENSE
+share/doc/searchjoin/README
+share/doc/seqan_tcoffee/LICENSE
+share/doc/seqan_tcoffee/README
+share/doc/seqan_tcoffee/example/seq.fa
+share/doc/seqcons2/LICENSE
+share/doc/seqcons2/README
+share/doc/sgip/LICENSE
+share/doc/sgip/README
+share/doc/sgip/example/iso_m2D_m196.A01
+share/doc/sgip/example/iso_r01_m200.A00
+share/doc/sgip/example/iso_r01_m200.A01
+share/doc/sgip/example/iso_r01_m200.B00
+share/doc/sgip/example/iso_r01_m200.B01
+share/doc/sgip/example/latin-4
+share/doc/sgip/example/lattice-4
+share/doc/sgip/example/sts-7
+share/doc/snp_store/LICENSE
+share/doc/snp_store/README
+share/doc/snp_store/example/exampleGenome.fa
+share/doc/snp_store/example/exampleReads.gff
+%%RM_I386%%share/doc/splazers/LICENSE
+%%RM_I386%%share/doc/splazers/README
+%%RM_I386%%share/doc/splazers/example/genome.fa
+%%RM_I386%%share/doc/splazers/example/reads.fa
+%%RM_I386%%share/doc/splazers/example/reads.fa.result
+share/doc/stellar/LICENSE
+share/doc/stellar/README
+share/doc/stellar/example/NC_001474.fasta
+share/doc/stellar/example/NC_001477.fasta
+share/doc/stellar/example/reads.fasta
+share/doc/tree_recon/LICENSE
+share/doc/tree_recon/README
+share/doc/tree_recon/example/example.dist
+share/doc/yara/LICENSE
+share/doc/yara/README.rst