wip/nanocomp: import nanocomp version 1.15.0.20210602 as wip/nanocomp

[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 07:01:39 2021 -0600
Changeset:	0fb29b04ade345ba8d9b300f73249a44ecee85e7

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

Log Message:
wip/nanocomp: import nanocomp version 1.15.0.20210602 as wip/nanocomp

Compare multiple runs of long read sequencing data and
alignments. Creates violin plots or box plots of length, quality and
percent identity and creates dynamic, overlaying read length
histograms and a cumulative yield plot.

As of version 1.1.0 NanoComp will also create a static png image for
dynamic html plots, as the latter can get quite big and slow to load
for big datasets. This however requires that you install orca
(https://github.com/plotly/orca). Without orca the script still works,
but no static copies of dynamic plots are created.

I welcome all suggestions, bug reports, feature requests and
contributions. Please leave an issue
(https://github.com/wdecoster/nanocomp/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=0fb29b04ade345ba8d9b300f73249a44ecee85e7

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

diffstat:
 Makefile          |  1 +
 nanocomp/DESCR    | 18 ++++++++++++++++++
 nanocomp/Makefile | 37 +++++++++++++++++++++++++++++++++++++
 nanocomp/PLIST    | 23 +++++++++++++++++++++++
 nanocomp/distinfo |  6 ++++++
 5 files changed, 85 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 3551167cca..99c85c6d2f 100644
--- a/Makefile
+++ b/Makefile
@@ -2464,6 +2464,7 @@ SUBDIR+=	naev
 SUBDIR+=	nag
 SUBDIR+=	nagios-plugin-mysql_health
 SUBDIR+=	nanoQC
+SUBDIR+=	nanocomp
 SUBDIR+=	nanofilt
 SUBDIR+=	nanoget
 SUBDIR+=	nanolyse
diff --git a/nanocomp/DESCR b/nanocomp/DESCR
new file mode 100644
index 0000000000..ba43e98e61
--- /dev/null
+++ b/nanocomp/DESCR
@@ -0,0 +1,18 @@
+Compare multiple runs of long read sequencing data and
+alignments. Creates violin plots or box plots of length, quality and
+percent identity and creates dynamic, overlaying read length
+histograms and a cumulative yield plot.
+
+As of version 1.1.0 NanoComp will also create a static png image for
+dynamic html plots, as the latter can get quite big and slow to load
+for big datasets. This however requires that you install orca
+(https://github.com/plotly/orca). Without orca the script still works,
+but no static copies of dynamic plots are created.
+
+I welcome all suggestions, bug reports, feature requests and
+contributions. Please leave an issue
+(https://github.com/wdecoster/nanocomp/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/nanocomp/Makefile b/nanocomp/Makefile
new file mode 100644
index 0000000000..522066254d
--- /dev/null
+++ b/nanocomp/Makefile
@@ -0,0 +1,37 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	nanocomp
+GITHUB_TAG=	45340db
+DISTNAME=	NanoComp-1.15.0.20210602
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/NanoComp
+COMMENT=	Compare runs of Oxford Nanopore sequencing data and alignments
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	${PYPKGPREFIX}-pandas>=1.2.4:../../math/py-pandas
+DEPENDS+=	nanoget>=1.4.0:../../wip/nanoget
+DEPENDS+=	nanomath>=1.0.0:../../wip/nanomath
+DEPENDS+=	NanoPlot>=1.38.0:../../wip/nanoplot
+DEPENDS+=	${PYPKGPREFIX}-psutil>=5.8.0:../../sysutils/py-psutil
+DEPENDS+=	${PYPKGPREFIX}-plotly>=3.4.2:../../wip/py-plotly
+DEPENDS+=	${PYPKGPREFIX}-seaborn>=0.9.0:../../graphics/py-seaborn
+DEPENDS+=	${PYPKGPREFIX}-matplotlib>=2.1.0:../../graphics/py-matplotlib
+DEPENDS+=	${PYPKGPREFIX}-joypy>=0.2.2:../../wip/py-joypy
+DEPENDS+=	${PYPKGPREFIX}-arrow>=0.15.8:../../time/py-arrow
+
+WRKSRC=		${WRKDIR}/nanocomp-45340dbe0c56d3fc1c5bf81a7dd485b5fbec68cf
+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/nanocomp/PLIST b/nanocomp/PLIST
new file mode 100644
index 0000000000..f64c2a8e5f
--- /dev/null
+++ b/nanocomp/PLIST
@@ -0,0 +1,23 @@
+@comment $NetBSD$
+bin/NanoComp
+${PYSITELIB}/${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
+${PYSITELIB}/nanocomp/NanoComp.py
+${PYSITELIB}/nanocomp/NanoComp.pyc
+${PYSITELIB}/nanocomp/NanoComp.pyo
+${PYSITELIB}/nanocomp/__init__.py
+${PYSITELIB}/nanocomp/__init__.pyc
+${PYSITELIB}/nanocomp/__init__.pyo
+${PYSITELIB}/nanocomp/compplots.py
+${PYSITELIB}/nanocomp/compplots.pyc
+${PYSITELIB}/nanocomp/compplots.pyo
+${PYSITELIB}/nanocomp/utils.py
+${PYSITELIB}/nanocomp/utils.pyc
+${PYSITELIB}/nanocomp/utils.pyo
+${PYSITELIB}/nanocomp/version.py
+${PYSITELIB}/nanocomp/version.pyc
+${PYSITELIB}/nanocomp/version.pyo
diff --git a/nanocomp/distinfo b/nanocomp/distinfo
new file mode 100644
index 0000000000..f52b12f04a
--- /dev/null
+++ b/nanocomp/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanocomp/NanoComp-1.15.0.20210602-45340db.tar.gz) = 474619b3c5feee17503d834c2dac7c3f59cd05e8
+RMD160 (nanocomp/NanoComp-1.15.0.20210602-45340db.tar.gz) = bc6667919c08d45c245314c76d3c6aedab809d34
+SHA512 (nanocomp/NanoComp-1.15.0.20210602-45340db.tar.gz) = e8a3a84d03404e753f99617b60156db2d982ab26efd8f0c189d6ddb9efd95607f1824ea5e5a7cf437c694ab8d28d9662cf54c757210bf5dea66fbd20609a6b53
+Size (nanocomp/NanoComp-1.15.0.20210602-45340db.tar.gz) = 175119 bytes