wip/nanostat: import nanostat version 1.5.0.20210108 as wip/nanostat

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Jun 7 18:22:11 2021 -0600
Changeset:	9ef7456d9c19632cd737d2bd38ebdb7c7d884b1c

Modified Files:
	Makefile
Added Files:
	nanostat/DESCR
	nanostat/Makefile
	nanostat/PLIST
	nanostat/distinfo

Log Message:
wip/nanostat: import nanostat version 1.5.0.20210108 as wip/nanostat

# NanoStat

Calculate various statistics from a long read sequencing dataset in
fastq, bam or albacore sequencing summary format.

#### Examples

NanoStat --fastq reads.fastq.gz --outdir statreports

NanoStat --summary sequencing_summary1.txt sequencing_summary2.txt \
	 sequencing_summary3.txt --readtype 1D2

NanoStat --bam alignment.bam alignment2.bam

I welcome all suggestions, bug reports, feature requests and
contributions. Please leave an issue
(https://github.com/wdecoster/nanostat/issues) or open a pull request.

If you use this tool, please consider citing our publication:
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9ef7456d9c19632cd737d2bd38ebdb7c7d884b1c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile          |  1 +
 nanostat/DESCR    | 20 ++++++++++++++++++++
 nanostat/Makefile | 29 +++++++++++++++++++++++++++++
 nanostat/PLIST    | 17 +++++++++++++++++
 nanostat/distinfo |  6 ++++++
 5 files changed, 73 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 992cfab04b..09124e1235 100644
--- a/Makefile
+++ b/Makefile
@@ -2465,6 +2465,7 @@ SUBDIR+=	nag
 SUBDIR+=	nagios-plugin-mysql_health
 SUBDIR+=	nanoget
 SUBDIR+=	nanomath
+SUBDIR+=	nanostat
 SUBDIR+=	naqsh-ttf
 SUBDIR+=	nary
 SUBDIR+=	natali
diff --git a/nanostat/DESCR b/nanostat/DESCR
new file mode 100644
index 0000000000..0ae584b801
--- /dev/null
+++ b/nanostat/DESCR
@@ -0,0 +1,20 @@
+# NanoStat
+
+Calculate various statistics from a long read sequencing dataset in
+fastq, bam or albacore sequencing summary format.
+
+#### Examples
+
+NanoStat --fastq reads.fastq.gz --outdir statreports
+
+NanoStat --summary sequencing_summary1.txt sequencing_summary2.txt \
+	 sequencing_summary3.txt --readtype 1D2
+
+NanoStat --bam alignment.bam alignment2.bam
+
+I welcome all suggestions, bug reports, feature requests and
+contributions. Please leave an issue
+(https://github.com/wdecoster/nanostat/issues) or open a pull request.
+
+If you use this tool, please consider citing our publication:
+https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939.
diff --git a/nanostat/Makefile b/nanostat/Makefile
new file mode 100644
index 0000000000..c3daae681f
--- /dev/null
+++ b/nanostat/Makefile
@@ -0,0 +1,29 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	nanostat
+GITHUB_TAG=	f50c753
+DISTNAME=	NanoStat-1.5.0.20210108
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/nanostat
+COMMENT=	Statistics for Oxford Nanopore sequencing data and alignments
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	nanoget>=1.12.2:../../wip/nanoget
+DEPENDS+=	nanomath>=1.0.0:../../wip/nanomath
+DEPENDS+=	${PYPKGPREFIX}-pysam>=0.15.1:../../wip/py-pysam
+
+WRKSRC=		${WRKDIR}/nanostat-f50c7530f072e9e2b3c830334d806a619dc37c68
+USE_LANGUAGES=	# none
+
+EGG_NAME=	${DISTNAME:C/\.[[:digit:]]+$$//}
+
+post-install:
+	${RM} -r ${DESTDIR}${PREFIX}/${PYSITELIB}/scripts
+
+.include "../../lang/python/egg.mk"
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/nanostat/PLIST b/nanostat/PLIST
new file mode 100644
index 0000000000..18b5da577a
--- /dev/null
+++ b/nanostat/PLIST
@@ -0,0 +1,17 @@
+@comment $NetBSD$
+bin/NanoStat
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/nanostat/NanoStat.py
+${PYSITELIB}/nanostat/NanoStat.pyc
+${PYSITELIB}/nanostat/NanoStat.pyo
+${PYSITELIB}/nanostat/__init__.py
+${PYSITELIB}/nanostat/__init__.pyc
+${PYSITELIB}/nanostat/__init__.pyo
+${PYSITELIB}/nanostat/version.py
+${PYSITELIB}/nanostat/version.pyc
+${PYSITELIB}/nanostat/version.pyo
diff --git a/nanostat/distinfo b/nanostat/distinfo
new file mode 100644
index 0000000000..4552970af5
--- /dev/null
+++ b/nanostat/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanostat/NanoStat-1.5.0.20210108-f50c753.tar.gz) = 490529cf921d20b8582cf30d48b9ae8e70301015
+RMD160 (nanostat/NanoStat-1.5.0.20210108-f50c753.tar.gz) = c7b997bda0a6a1e07f8d8e1f748a34f2950c46d6
+SHA512 (nanostat/NanoStat-1.5.0.20210108-f50c753.tar.gz) = 6572368d6ad30ce5d69e2ed9fa0b6bb8208643829e59d1be2387072fc00e926568c904af25f4535812ea2409161724949708946ae1ed48839c90c31524e7c394
+Size (nanostat/NanoStat-1.5.0.20210108-f50c753.tar.gz) = 17534 bytes