From owner-svn-ports-head@freebsd.org Tue May 10 00:52:06 2016 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 0F573B336D9; Tue, 10 May 2016 00:52:06 +0000 (UTC) (envelope-from junovitch@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id DFD271395; Tue, 10 May 2016 00:52:05 +0000 (UTC) (envelope-from junovitch@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u4A0q5ID095305; Tue, 10 May 2016 00:52:05 GMT (envelope-from junovitch@FreeBSD.org) Received: (from junovitch@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u4A0q4Nv095300; Tue, 10 May 2016 00:52:04 GMT (envelope-from junovitch@FreeBSD.org) Message-Id: <201605100052.u4A0q4Nv095300@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: junovitch set sender to junovitch@FreeBSD.org using -f From: Jason Unovitch Date: Tue, 10 May 2016 00:52:04 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r414897 - in head/biology: . seqan-apps X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.22 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 10 May 2016 00:52:06 -0000 Author: junovitch Date: Tue May 10 00:52:04 2016 New Revision: 414897 URL: https://svnweb.freebsd.org/changeset/ports/414897 Log: 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 Added: head/biology/seqan-apps/ head/biology/seqan-apps/Makefile (contents, props changed) head/biology/seqan-apps/distinfo (contents, props changed) head/biology/seqan-apps/pkg-descr (contents, props changed) head/biology/seqan-apps/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue May 10 00:22:27 2016 (r414896) +++ head/biology/Makefile Tue May 10 00:52:04 2016 (r414897) @@ -90,6 +90,7 @@ SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan + SUBDIR += seqan-apps SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 Added: head/biology/seqan-apps/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqan-apps/Makefile Tue May 10 00:52:04 2016 (r414897) @@ -0,0 +1,46 @@ +# Created by: Hannes Hauswedell +# $FreeBSD$ + +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 + +.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 Added: head/biology/seqan-apps/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqan-apps/distinfo Tue May 10 00:52:04 2016 (r414897) @@ -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 Added: head/biology/seqan-apps/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqan-apps/pkg-descr Tue May 10 00:52:04 2016 (r414897) @@ -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/ Added: head/biology/seqan-apps/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/seqan-apps/pkg-plist Tue May 10 00:52:04 2016 (r414897) @@ -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