wip/nanopack: import nanopack version 0.0.0.20210524 as wip/nanopack

[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 07:07:29 2021 -0600
Changeset:	80e16121d732f5183079987be478be78501893d9

Modified Files:
	Makefile
Added Files:
	nanopack/DESCR
	nanopack/Makefile

Log Message:
wip/nanopack: import nanopack version 0.0.0.20210524 as wip/nanopack

This is a meta package that depends on all components of NanoPack.

NanoComp: comparing multiple runs on read length and quality based on
reads (fastq), alignments (bam) or albacore summary files.

NanoFilt: Streaming script for filtering a fastq file based on a
minimum length, minimum quality cut-off, minimum and maximum average
GC. Also trimming nucleotides from either read ends is an option.

NanoLyse: Streaming script for filtering a fastq file to remove reads
mapping to the lambda phage genome (control DNA used in nanopore
sequencing). Uses minimap2/mappy.

NanoPlot: creating many relevant plots derived from reads (fastq),
alignments (bam) and albacore summary files. Examples can be found in
the gallery on my blog. NanoPack is also available with a graphical
user interface in NanoGUI or as a web service.

NanoQC: Generating plots to investigate nucleotide composition and
quality distribution at the end of reads.

NanoStat: Quickly create a statistical summary from reads, an
alignment or a summary file.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=80e16121d732f5183079987be478be78501893d9

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

diffstat:
 Makefile          |  1 +
 nanopack/DESCR    | 23 +++++++++++++++++++++++
 nanopack/Makefile | 21 +++++++++++++++++++++
 3 files changed, 45 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 99c85c6d2f..9dabaea2fd 100644
--- a/Makefile
+++ b/Makefile
@@ -2469,6 +2469,7 @@ SUBDIR+=	nanofilt
 SUBDIR+=	nanoget
 SUBDIR+=	nanolyse
 SUBDIR+=	nanomath
+SUBDIR+=	nanopack
 SUBDIR+=	nanoplot
 SUBDIR+=	nanostat
 SUBDIR+=	naqsh-ttf
diff --git a/nanopack/DESCR b/nanopack/DESCR
new file mode 100644
index 0000000000..7a19cbeb67
--- /dev/null
+++ b/nanopack/DESCR
@@ -0,0 +1,23 @@
+This is a meta package that depends on all components of NanoPack.
+
+NanoComp: comparing multiple runs on read length and quality based on
+reads (fastq), alignments (bam) or albacore summary files.
+
+NanoFilt: Streaming script for filtering a fastq file based on a
+minimum length, minimum quality cut-off, minimum and maximum average
+GC. Also trimming nucleotides from either read ends is an option.
+
+NanoLyse: Streaming script for filtering a fastq file to remove reads
+mapping to the lambda phage genome (control DNA used in nanopore
+sequencing). Uses minimap2/mappy.
+
+NanoPlot: creating many relevant plots derived from reads (fastq),
+alignments (bam) and albacore summary files. Examples can be found in
+the gallery on my blog. NanoPack is also available with a graphical
+user interface in NanoGUI or as a web service.
+
+NanoQC: Generating plots to investigate nucleotide composition and
+quality distribution at the end of reads.
+
+NanoStat: Quickly create a statistical summary from reads, an
+alignment or a summary file.
diff --git a/nanopack/Makefile b/nanopack/Makefile
new file mode 100644
index 0000000000..19358a3390
--- /dev/null
+++ b/nanopack/Makefile
@@ -0,0 +1,21 @@
+# $NetBSD$
+
+META_PACKAGE=	yes
+
+PKGNAME=	nanopack-0.0.0.20210524
+CATEGORIES+=	meta-pkgs biology
+MASTER_SITES=	# empty
+DISTFILES=	# empty
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/wdecoster/nanopack
+COMMENT=	Long read processing and analysis scripts
+
+DEPENDS+=	NanoComp>=1.12.0:../../wip/nanocomp
+DEPENDS+=	NanoFilt>=2.6.0:../../wip/nanofilt
+DEPENDS+=	NanoLyse>=1.2.0:../../wip/nanolyse
+DEPENDS+=	NanoPlot>=1.33.0:../../wip/nanoplot
+DEPENDS+=	NanoStat>=1.4.0:../../wip/nanostat
+DEPENDS+=	nanoQC>=0.0.0.20210522:../../wip/nanoQC
+
+.include "../../mk/bsd.pkg.mk"