svn commit: r414897 - in head/biology: . seqan-apps
Jason Unovitch
junovitch at FreeBSD.org
Tue May 10 00:52:06 UTC 2016
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 <h2+fbsdports at fsfe.org>
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 <h2+fbsdports at fsfe.org>
+# $FreeBSD$
+
+PORTNAME= seqan-apps
+PORTVERSION= 2.1.1
+DISTVERSIONPREFIX= seqan-v
+CATEGORIES= biology
+
+MAINTAINER= h2+fbsdports at 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>
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
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