wip/nanolyse: import nanolyse version 1.2.0.20200915 as wip/nanolyse

[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 06:51:44 2021 -0600
Changeset:	f1bd2d62b3bb2e6694d396d0be41e88f7b71d191

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

Log Message:
wip/nanolyse: import nanolyse version 1.2.0.20200915 as wip/nanolyse

Remove reads mapping to the lambda phage genome from a fastq file.
This script uses Heng Li's minimap2 (https://github.com/lh3/minimap2)
and his mappy Python binding (https://pypi.python.org/pypi/mappy).

### Warning

If (some of) the reads of your genome of interest are sufficiently
similar to the lambda genome those reads will be lost.

### Examples

gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz

In combination with NanoFilt (https://github.com/wdecoster/nanofilt):

gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 \
       | gzip > filtered_reads_without_lambda.fastq.gz

Using a different genome to filter on (rather than lambda phage):

gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz \
       | gzip > reads_without_mygenome.fastq.gz

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f1bd2d62b3bb2e6694d396d0be41e88f7b71d191

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

diffstat:
 Makefile          |  1 +
 nanolyse/DESCR    | 22 ++++++++++++++++++++++
 nanolyse/Makefile | 24 ++++++++++++++++++++++++
 nanolyse/PLIST    | 18 ++++++++++++++++++
 nanolyse/distinfo |  6 ++++++
 5 files changed, 71 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 61cb336f07..1d1e77a896 100644
--- a/Makefile
+++ b/Makefile
@@ -2465,6 +2465,7 @@ SUBDIR+=	nag
 SUBDIR+=	nagios-plugin-mysql_health
 SUBDIR+=	nanofilt
 SUBDIR+=	nanoget
+SUBDIR+=	nanolyse
 SUBDIR+=	nanomath
 SUBDIR+=	nanostat
 SUBDIR+=	naqsh-ttf
diff --git a/nanolyse/DESCR b/nanolyse/DESCR
new file mode 100644
index 0000000000..6e85d144db
--- /dev/null
+++ b/nanolyse/DESCR
@@ -0,0 +1,22 @@
+Remove reads mapping to the lambda phage genome from a fastq file.
+This script uses Heng Li's minimap2 (https://github.com/lh3/minimap2)
+and his mappy Python binding (https://pypi.python.org/pypi/mappy).
+
+### Warning
+
+If (some of) the reads of your genome of interest are sufficiently
+similar to the lambda genome those reads will be lost.
+
+### Examples
+
+gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz
+
+In combination with NanoFilt (https://github.com/wdecoster/nanofilt):
+
+gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 \
+       | gzip > filtered_reads_without_lambda.fastq.gz
+
+Using a different genome to filter on (rather than lambda phage):
+
+gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz \
+       | gzip > reads_without_mygenome.fastq.gz
diff --git a/nanolyse/Makefile b/nanolyse/Makefile
new file mode 100644
index 0000000000..698d5ebacd
--- /dev/null
+++ b/nanolyse/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	nanolyse
+GITHUB_TAG=	a3de1e9
+DISTNAME=	NanoLyse-1.2.0.20200915
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=wdecoster/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/nanolyse
+COMMENT=	Removing reads mapping to the lambda genome
+LICENSE=	gnu-gpl-v3
+
+DEPENDS+=	${PYPKGPREFIX}-biopython>=1.74:../../biology/py-biopython
+DEPENDS+=	${PYPKGPREFIX}-mappy>=2.18:../../biology/py-mappy
+
+WRKSRC=		${WRKDIR}/nanolyse-a3de1e9c81aeddf15ef985486ca80b6876674948
+USE_LANGUAGES=	# none
+
+EGG_NAME=	${DISTNAME:C/\.[[:digit:]]+$$//}
+
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/nanolyse/PLIST b/nanolyse/PLIST
new file mode 100644
index 0000000000..94de3eff59
--- /dev/null
+++ b/nanolyse/PLIST
@@ -0,0 +1,18 @@
+@comment $NetBSD$
+bin/NanoLyse
+${PYSITELIB}/${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
+${PYSITELIB}/nanolyse/NanoLyse.py
+${PYSITELIB}/nanolyse/NanoLyse.pyc
+${PYSITELIB}/nanolyse/NanoLyse.pyo
+${PYSITELIB}/nanolyse/__init__.py
+${PYSITELIB}/nanolyse/__init__.pyc
+${PYSITELIB}/nanolyse/__init__.pyo
+${PYSITELIB}/nanolyse/version.py
+${PYSITELIB}/nanolyse/version.pyc
+${PYSITELIB}/nanolyse/version.pyo
+${PYSITELIB}/reference/lambda.fasta.gz
diff --git a/nanolyse/distinfo b/nanolyse/distinfo
new file mode 100644
index 0000000000..bfa5a8e280
--- /dev/null
+++ b/nanolyse/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (nanolyse/NanoLyse-1.2.0.20200915-a3de1e9.tar.gz) = 953470f2931639f54bdbf6f068fbd738c70c6215
+RMD160 (nanolyse/NanoLyse-1.2.0.20200915-a3de1e9.tar.gz) = 03a4043a8cc5bb68e752d531de8e4a17291199e3
+SHA512 (nanolyse/NanoLyse-1.2.0.20200915-a3de1e9.tar.gz) = 7a0f02611ca74c01689e5b796983e828580adb59b40633ff6cd64cfa7210c767a809282ce1c7d91fff7dade414f37e336dbed8ae395855d7e9714cd2e5a42ac1
+Size (nanolyse/NanoLyse-1.2.0.20200915-a3de1e9.tar.gz) = 34153 bytes