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freebsd-ports/biology/samtools/Makefile

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Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
# Created by: Reed A. Cartwright <cartwright@asu.edu>
# $FreeBSD$
PORTNAME= samtools
biology/samtools: update to 1.9 PR: 230171 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16569
2018-08-02 21:28:36 +02:00
DISTVERSION= 1.9
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
biology/htslib biology/bcftools biology/samtools: Update to 1.6 PR: 223094 Submitted by: mzaki@niid.go.jp Approved by: cartwright@asu.edu (maintainer) Approved by: olivier (mentor) Differential Revision: https://reviews.freebsd.org/D12768
2017-10-25 12:19:50 +02:00
BUILD_DEPENDS= htslib>=1.6:biology/htslib
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. With hat: portmgr Sponsored by: Absolight
2016-04-01 15:29:15 +02:00
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
biology/samtools: update to 1.9 PR: 230171 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16569
2018-08-02 21:28:36 +02:00
USES= autoreconf gmake localbase ncurses \
perl5 python:env shebangfix
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
USE_GITHUB= yes
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require version 1.3 of htslib. - Add CURL option to htslib - Add TEST_TARGET with perl and bash dependencies for testing - Tidy up spacing and pkg-message's PR: 205524 PR: 205525 PR: 205526 Submitted by: cartwright@asu.edu (maintainer)
2015-12-25 02:31:09 +01:00
USE_PERL5= test
GNU_CONFIGURE= yes
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
SUB_FILES= pkg-message
biology/htslib biology/bcftools biology/samtools: Update to 1.6 PR: 223094 Submitted by: mzaki@niid.go.jp Approved by: cartwright@asu.edu (maintainer) Approved by: olivier (mentor) Differential Revision: https://reviews.freebsd.org/D12768
2017-10-25 12:19:50 +02:00
SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require version 1.3 of htslib. - Add CURL option to htslib - Add TEST_TARGET with perl and bash dependencies for testing - Tidy up spacing and pkg-message's PR: 205524 PR: 205525 PR: 205526 Submitted by: cartwright@asu.edu (maintainer)
2015-12-25 02:31:09 +01:00
TEST_TARGET= test
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
.include <bsd.port.mk>
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