From 288c7727d2e4f9517fe3572cdec2562f6c3c6ea1 Mon Sep 17 00:00:00 2001 From: junovitch Date: Tue, 10 May 2016 00:52:04 +0000 Subject: 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 --- biology/Makefile | 1 + biology/seqan-apps/Makefile | 46 +++++++++++++ biology/seqan-apps/distinfo | 2 + biology/seqan-apps/pkg-descr | 11 +++ biology/seqan-apps/pkg-plist | 160 +++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 220 insertions(+) create mode 100644 biology/seqan-apps/Makefile create mode 100644 biology/seqan-apps/distinfo create mode 100644 biology/seqan-apps/pkg-descr create mode 100644 biology/seqan-apps/pkg-plist (limited to 'biology') 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 +# $FreeBSD$ + +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 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 -- cgit