Re: Import tophat-2.1.1 as wip/tophat.

[Thomas Klausner <wiz%NetBSD.org@localhost>]

On Wed, May 11, 2016 at 03:26:53PM +0000, Jason Bacon wrote:
> Module Name:	pkgsrc-wip
> Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
> Pushed By:	outpaddling
> Date:		Wed May 11 10:26:53 2016 -0500
> Changeset:	f93b6b393abf75ca8912351ae2b5e32634ba93ec
> 
> Added Files:
> 	tophat/DESCR
> 	tophat/Makefile
> 	tophat/PLIST
> 	tophat/TODO
> 	tophat/distinfo
> 	tophat/patches/patch-src-bam_merge.cpp
> 	tophat/patches/patch-src-samtools-0.1.18-Makefile
> 	tophat/patches/patch-src_Makefile.in
> 
> Log Message:
> Import tophat-2.1.1 as wip/tophat.
> 
> TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
> reads to mammalian-sized genomes using the ultra high-throughput short read
> aligner Bowtie, and then analyzes the mapping results to identify splice
> junctions between exons.
> 
> To see a diff of this commit:
> https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f93b6b393abf75ca8912351ae2b5e32634ba93ec
> 
> Please note that diffs are not public domain; they are subject to the
> copyright notices on the relevant files.
> 
> diffstat:
>  tophat/DESCR                                      |  4 +++
>  tophat/Makefile                                   | 40 +++++++++++++++++++++++
>  tophat/PLIST                                      | 29 ++++++++++++++++
>  tophat/TODO                                       |  1 +
>  tophat/distinfo                                   |  9 +++++
>  tophat/patches/patch-src-bam_merge.cpp            | 10 ++++++
>  tophat/patches/patch-src-samtools-0.1.18-Makefile | 28 ++++++++++++++++
>  tophat/patches/patch-src_Makefile.in              | 23 +++++++++++++
>  8 files changed, 144 insertions(+)
> 
> diffs:
> diff --git a/tophat/DESCR b/tophat/DESCR
> new file mode 100644
> index 0000000..5ec85b9
> --- /dev/null
> +++ b/tophat/DESCR
> @@ -0,0 +1,4 @@
> +TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
> +reads to mammalian-sized genomes using the ultra high-throughput short read
> +aligner Bowtie, and then analyzes the mapping results to identify splice
> +junctions between exons.
> diff --git a/tophat/Makefile b/tophat/Makefile
> new file mode 100644
> index 0000000..ddd1394
> --- /dev/null
> +++ b/tophat/Makefile
> @@ -0,0 +1,40 @@
> +# $NetBSD$
> +#
> +###########################################################
> +#                  Generated by fbsd2pkg                  #
> +#              Thu Mar  3 09:54:03 CST 2016               #
> +###########################################################
> +
> +DISTNAME=	tophat-${PORTVERSION}
> +CATEGORIES=	biology
> +# Note: Distfiles on Github are not the same as those here
> +MASTER_SITES=	http://ccb.jhu.edu/software/tophat/downloads/
> +
> +MAINTAINER=	bacon4000%gmail.com@localhost
> +HOMEPAGE=	http://ccb.jhu.edu/software/tophat/index.shtml
> +COMMENT=	Fast splice junction mapper for RNA-Seq reads
> +LICENSE=	boost-license
> +
> +MAKE_JOBS_SAFE=	no
> +
> +DEPENDS+=	bowtie2>=0:../../wip/bowtie2
> +
> +USE_LANGUAGES=	c c++
> +USE_TOOLS+=	gmake
> +GNU_CONFIGURE=	yes
> +
> +REPLACE_PYTHON=	src/bed_to_juncs \
> +		src/contig_to_chr_coords \
> +		src/sra_to_solid \
> +		src/tophat-fusion-post \
> +		src/tophat.py

Similarly here, multiple lines with REPLACE_PYTHON+=

The advantage is that grep finds everything in one line.

> +PORTVERSION=	2.1.1

We usually have this in DISTNAME, PKGVERSION and PKGVERSION_NOREV are
then automatically defined by the framework.
 Thomas