wip/nanoget: import nanoget version 1.16.1.20210320 as wip/nanoget

[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 18:19:40 2021 -0600
Changeset:	266c9bf220a0728eb738954496f62f42eb74a176

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

Log Message:
wip/nanoget: import nanoget version 1.16.1.20210320 as wip/nanoget

Nanoget provides functions to extract useful metrics from Oxford
Nanopore sequencing reads and alignments.

## Functions

Data can be presented in the following formats, using the following
functions:

- A sorted bam file `process_bam(bamfile, threads)`
- A standard fastq file `process_fastq_plain(fastqfile, 'threads')`
- A fastq file with metadata from MinKNOW or Albacore
  `process_fastq_rich(fastqfile)`
- A sequencing_summary file generated by Albacore
  `process_summary(sequencing_summary.txt, 'readtype')`

Fastq files can be compressed using gzip, bzip2 or bgzip. The data is
returned as a pandas DataFrame with standardized headernames for
convenient extraction. The functions perform logging while being
called and extracting data.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=266c9bf220a0728eb738954496f62f42eb74a176

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

diffstat:
 Makefile         |  1 +
 nanoget/DESCR    | 19 +++++++++++++++++++
 nanoget/Makefile | 32 ++++++++++++++++++++++++++++++++
 nanoget/PLIST    | 21 +++++++++++++++++++++
 nanoget/distinfo |  6 ++++++
 5 files changed, 79 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 49823d5215..992cfab04b 100644
--- a/Makefile
+++ b/Makefile
@@ -2463,6 +2463,7 @@ SUBDIR+=	n2n
 SUBDIR+=	naev
 SUBDIR+=	nag
 SUBDIR+=	nagios-plugin-mysql_health
+SUBDIR+=	nanoget
 SUBDIR+=	nanomath
 SUBDIR+=	naqsh-ttf
 SUBDIR+=	nary
diff --git a/nanoget/DESCR b/nanoget/DESCR
new file mode 100644
index 0000000000..d8440ce749
--- /dev/null
+++ b/nanoget/DESCR
@@ -0,0 +1,19 @@
+Nanoget provides functions to extract useful metrics from Oxford
+Nanopore sequencing reads and alignments.
+
+## Functions
+
+Data can be presented in the following formats, using the following
+functions:
+
+- A sorted bam file `process_bam(bamfile, threads)`
+- A standard fastq file `process_fastq_plain(fastqfile, 'threads')`
+- A fastq file with metadata from MinKNOW or Albacore
+  `process_fastq_rich(fastqfile)`
+- A sequencing_summary file generated by Albacore
+  `process_summary(sequencing_summary.txt, 'readtype')`
+
+Fastq files can be compressed using gzip, bzip2 or bgzip. The data is
+returned as a pandas DataFrame with standardized headernames for
+convenient extraction. The functions perform logging while being
+called and extracting data.
diff --git a/nanoget/Makefile b/nanoget/Makefile
new file mode 100644
index 0000000000..25d460e749
--- /dev/null
+++ b/nanoget/Makefile
@@ -0,0 +1,32 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	nanoget
+GITHUB_TAG=	e130bb0
+DISTNAME=	nanoget-1.16.1.20210320
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/nanoget
+COMMENT=	Extract information from Oxford Nanopore sequencing data
+LICENSE=	mit
+
+DEPENDS+=	${PYPKGPREFIX}-pandas>=0.22.0:../../math/py-pandas
+DEPENDS+=	${PYPKGPREFIX}-biopython>=1.74:../../biology/py-biopython
+DEPENDS+=	${PYPKGPREFIX}-pysam>=0.16.0:../../wip/py-pysam
+DEPENDS+=	nanomath>=1.0.1:../../wip/nanomath
+
+WRKSRC=		${WRKDIR}/nanoget-e130bb016f7af7844e7d4145f05f62360ebcd6dd
+USE_LANGUAGES=	# none
+
+EGG_NAME=	${DISTNAME:C/\.[[:digit:]]+$$//}
+
+post-install:
+	rm ${DESTDIR}${PREFIX}/LICENSE
+	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/nanoget/PLIST b/nanoget/PLIST
new file mode 100644
index 0000000000..ad8aa94898
--- /dev/null
+++ b/nanoget/PLIST
@@ -0,0 +1,21 @@
+@comment $NetBSD$
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/nanoget/__init__.py
+${PYSITELIB}/nanoget/__init__.pyc
+${PYSITELIB}/nanoget/__init__.pyo
+${PYSITELIB}/nanoget/extraction_functions.py
+${PYSITELIB}/nanoget/extraction_functions.pyc
+${PYSITELIB}/nanoget/extraction_functions.pyo
+${PYSITELIB}/nanoget/nanoget.py
+${PYSITELIB}/nanoget/nanoget.pyc
+${PYSITELIB}/nanoget/nanoget.pyo
+${PYSITELIB}/nanoget/utils.py
+${PYSITELIB}/nanoget/utils.pyc
+${PYSITELIB}/nanoget/utils.pyo
+${PYSITELIB}/nanoget/version.py
+${PYSITELIB}/nanoget/version.pyc
+${PYSITELIB}/nanoget/version.pyo
diff --git a/nanoget/distinfo b/nanoget/distinfo
new file mode 100644
index 0000000000..390c7bbeee
--- /dev/null
+++ b/nanoget/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanoget/nanoget-1.16.1.20210320-e130bb0.tar.gz) = 4aeedf392d2433a5dc2a294d64c6c25693a250ec
+RMD160 (nanoget/nanoget-1.16.1.20210320-e130bb0.tar.gz) = cf7c0a607980da9e7e3f4630dd03fa1b392fcd11
+SHA512 (nanoget/nanoget-1.16.1.20210320-e130bb0.tar.gz) = 6ed5b35a8b196c7ab0fe00c7b15d4ac07799f22e619caf604f4d1273836deb048f3070b11da2b248a8266fdf0c8abfd0eb88291813e3063dffec442c128af842
+Size (nanoget/nanoget-1.16.1.20210320-e130bb0.tar.gz) = 22708 bytes