wip/nanoQC: import nanoQC version 0.9.4.20200617 as wip/nanoQC

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

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Tue Jun 8 06:54:36 2021 -0600
Changeset:	aee0e90213339afb794d57bdfbd70018bcca0de7

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

Log Message:
wip/nanoQC: import nanoQC version 0.9.4.20200617 as wip/nanoQC

Quality control tools for long read sequencing data aiming to
replicate some of the plots made by fastQC. This is an immature tool
and I welcome all contributions.

Creates dynamic plots using bokeh.  For an example see
http://decoster.xyz/wouter/.

nanoQC [-h] [-v] [-o OUTDIR] fastq

positional arguments:
  fastq                 Reads data in fastq.gz format.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Print version and exit.
  -o, --outdir OUTDIR   Specify directory in which output has to be created.
  -l, --minlen int      Minimum length of reads to be included in the plots
                        This also controls the length plotted in the graphs
                        from the beginning and end of reads
			(length plotted = minlen / 2)

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=aee0e90213339afb794d57bdfbd70018bcca0de7

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

diffstat:
 Makefile        |  1 +
 nanoQC/DESCR    | 23 +++++++++++++++++++++++
 nanoQC/Makefile | 30 ++++++++++++++++++++++++++++++
 nanoQC/PLIST    | 17 +++++++++++++++++
 nanoQC/distinfo |  6 ++++++
 5 files changed, 77 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 1d1e77a896..1d4186ac6a 100644
--- a/Makefile
+++ b/Makefile
@@ -2463,6 +2463,7 @@ SUBDIR+=	n2n
 SUBDIR+=	naev
 SUBDIR+=	nag
 SUBDIR+=	nagios-plugin-mysql_health
+SUBDIR+=	nanoQC
 SUBDIR+=	nanofilt
 SUBDIR+=	nanoget
 SUBDIR+=	nanolyse
diff --git a/nanoQC/DESCR b/nanoQC/DESCR
new file mode 100644
index 0000000000..34902dbfcb
--- /dev/null
+++ b/nanoQC/DESCR
@@ -0,0 +1,23 @@
+Quality control tools for long read sequencing data aiming to
+replicate some of the plots made by fastQC. This is an immature tool
+and I welcome all contributions.
+
+Creates dynamic plots using bokeh.  For an example see
+http://decoster.xyz/wouter/.
+
+nanoQC [-h] [-v] [-o OUTDIR] fastq
+
+positional arguments:
+  fastq                 Reads data in fastq.gz format.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -v, --version         Print version and exit.
+  -o, --outdir OUTDIR   Specify directory in which output has to be created.
+  -l, --minlen int      Minimum length of reads to be included in the plots
+                        This also controls the length plotted in the graphs
+                        from the beginning and end of reads
+			(length plotted = minlen / 2)
+
+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/nanoQC/Makefile b/nanoQC/Makefile
new file mode 100644
index 0000000000..6c7406fe32
--- /dev/null
+++ b/nanoQC/Makefile
@@ -0,0 +1,30 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	nanoQC
+GITHUB_TAG=	a7bcbdc
+DISTNAME=	nanoQC-0.9.4.20200617
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+EXTRACT_SUFX=	.zip
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/nanoQC
+COMMENT=	Create fastQC-like plots for Oxford Nanopore sequencing data
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	${PYPKGPREFIX}-biopython>=0:../../biology/py-biopython
+DEPENDS+=	${PYPKGPREFIX}-bokeh>=0:../../wip/py-bokeh
+
+WRKSRC=		${WRKDIR}/nanoQC-a7bcbdcec050b4ed1479fc740d5a931f9b9463b0
+USE_LANGUAGES=	# none
+
+EGG_NAME=	${DISTNAME:C/\.[[:digit:]]+$$//}
+
+post-install:
+	rm -r ${DESTDIR}${PREFIX}/${PYSITELIB}/scripts
+
+BUILDLINK_API_DEPENDS.py-numpy+=	${PYPKGPREFIX}-numpy>=1.20.3
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/nanoQC/PLIST b/nanoQC/PLIST
new file mode 100644
index 0000000000..baa11cb5bc
--- /dev/null
+++ b/nanoQC/PLIST
@@ -0,0 +1,17 @@
+@comment $NetBSD$
+bin/nanoQC
+${PYSITELIB}/${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
+${PYSITELIB}/nanoQC/__init__.py
+${PYSITELIB}/nanoQC/__init__.pyc
+${PYSITELIB}/nanoQC/__init__.pyo
+${PYSITELIB}/nanoQC/nanoQC.py
+${PYSITELIB}/nanoQC/nanoQC.pyc
+${PYSITELIB}/nanoQC/nanoQC.pyo
+${PYSITELIB}/nanoQC/version.py
+${PYSITELIB}/nanoQC/version.pyc
+${PYSITELIB}/nanoQC/version.pyo
diff --git a/nanoQC/distinfo b/nanoQC/distinfo
new file mode 100644
index 0000000000..00846e400b
--- /dev/null
+++ b/nanoQC/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanoQC/nanoQC-0.9.4.20200617-a7bcbdc.zip) = 488d8010a9516bbbc5e3c998bfeaaa26f05441c3
+RMD160 (nanoQC/nanoQC-0.9.4.20200617-a7bcbdc.zip) = 240c88523b4cb819d696201b81d8bb92c187ebb1
+SHA512 (nanoQC/nanoQC-0.9.4.20200617-a7bcbdc.zip) = 02c3e9e547b8f79d49f8aceef7ddf531d1602b69087169dd88ea96d3ae6c34a5e293067d7286163f771734f491516f1dcf1d70282eeb04367de46681372ecf6e
+Size (nanoQC/nanoQC-0.9.4.20200617-a7bcbdc.zip) = 19381 bytes