Date: Mon, 25 Feb 2019 07:56:45 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493842 - in head/biology: . abyss abyss/files Message-ID: <201902250756.x1P7ujXG080768@repo.freebsd.org>
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Author: yuri Date: Mon Feb 25 07:56:45 2019 New Revision: 493842 URL: https://svnweb.freebsd.org/changeset/ports/493842 Log: New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler Added: head/biology/abyss/ head/biology/abyss/Makefile (contents, props changed) head/biology/abyss/distinfo (contents, props changed) head/biology/abyss/files/ head/biology/abyss/files/patch-Common_Timer.h (contents, props changed) head/biology/abyss/pkg-descr (contents, props changed) head/biology/abyss/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Feb 25 07:07:45 2019 (r493841) +++ head/biology/Makefile Mon Feb 25 07:56:45 2019 (r493842) @@ -3,6 +3,7 @@ COMMENT = Biology + SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel Added: head/biology/abyss/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/abyss/Makefile Mon Feb 25 07:56:45 2019 (r493842) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= abyss +DISTVERSION= 2.1.5 +CATEGORIES= biology +MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \ + ghc:lang/ghc \ + pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer +LIB_DEPENDS= libffi.so:devel/libffi \ + libgmp.so:math/gmp \ + libomp.so:devel/openmp +RUN_DEPENDS= bash:shells/bash \ + gmake:devel/gmake + +USES= gmake iconv:wchar_t localbase:ldflags shebangfix sqlite +SHEBANG_FILES= bin/${PORTNAME}-* +SHEBANG_LANG= make +make_OLD_CMD= /usr/bin/make +make_CMD= ${PREFIX}/bin/gmake +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs + +OPTIONS_DEFINE= DOCS + +PORTDOCS= * + +.include <bsd.port.mk> Added: head/biology/abyss/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/abyss/distinfo Mon Feb 25 07:56:45 2019 (r493842) @@ -0,0 +1,3 @@ +TIMESTAMP = 1551061546 +SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757 +SIZE (abyss-2.1.5.tar.gz) = 1201318 Added: head/biology/abyss/files/patch-Common_Timer.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/abyss/files/patch-Common_Timer.h Mon Feb 25 07:56:45 2019 (r493842) @@ -0,0 +1,11 @@ +--- Common/Timer.h.orig 2019-02-25 02:35:12 UTC ++++ Common/Timer.h +@@ -3,6 +3,8 @@ + + #include <string> + ++#include <time.h> ++ + /** + * Time the duration between the construction and destruction of this + * timer object and log that duration. Added: head/biology/abyss/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/abyss/pkg-descr Mon Feb 25 07:56:45 2019 (r493842) @@ -0,0 +1,6 @@ +ABySS is a de novo, parallel, paired-end sequence assembler that is designed for +short reads. The single-processor version is useful for assembling genomes up to +100 Mbases in size. The parallel version is implemented using MPI and is capable +of assembling larger genomes. + +WWW: http://www.bcgsc.ca/platform/bioinfo/software/abyss Added: head/biology/abyss/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/abyss/pkg-plist Mon Feb 25 07:56:45 2019 (r493842) @@ -0,0 +1,60 @@ +bin/ABYSS +bin/ABYSS-P +bin/AdjList +bin/Consensus +bin/DAssembler +bin/DistanceEst +bin/DistanceEst-ssq +bin/KAligner +bin/MergeContigs +bin/MergePaths +bin/Overlap +bin/ParseAligns +bin/PathConsensus +bin/PathOverlap +bin/PopBubbles +bin/SimpleGraph +bin/abyss-align +bin/abyss-bloom +bin/abyss-bloom-dbg +bin/abyss-bloom-dist.mk +bin/abyss-bowtie +bin/abyss-bowtie2 +bin/abyss-bwa +bin/abyss-bwamem +bin/abyss-bwasw +bin/abyss-db-csv +bin/abyss-db-txt +bin/abyss-dida +bin/abyss-fac +bin/abyss-fatoagp +bin/abyss-filtergraph +bin/abyss-fixmate +bin/abyss-fixmate-ssq +bin/abyss-gapfill +bin/abyss-gc +bin/abyss-index +bin/abyss-junction +bin/abyss-kaligner +bin/abyss-layout +bin/abyss-longseqdist +bin/abyss-map +bin/abyss-map-ssq +bin/abyss-mergepairs +bin/abyss-overlap +bin/abyss-paired-dbg +bin/abyss-pe +bin/abyss-samtoafg +bin/abyss-samtobreak +bin/abyss-scaffold +bin/abyss-sealer +bin/abyss-stack-size +bin/abyss-tabtomd +bin/abyss-todot +bin/abyss-tofastq +bin/konnector +bin/logcounter +man/man1/ABYSS.1.gz +man/man1/abyss-pe.1.gz +man/man1/abyss-sealer.1.gz +man/man1/abyss-tofastq.1.gz
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