diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/seqan-apps/Makefile | 46 | ||||
| -rw-r--r-- | biology/seqan-apps/distinfo | 2 | ||||
| -rw-r--r-- | biology/seqan-apps/pkg-descr | 11 | ||||
| -rw-r--r-- | biology/seqan-apps/pkg-plist | 160 |
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 |