rna-seq: Meta-package for RNA-Seq differential gene expression

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Oct 28 07:22:16 2022 -0500
Changeset:	3bfdeb2c18878b9c19dcf2ca138d46bbca1035e9

Modified Files:
	Makefile
Added Files:
	rna-seq/DESCR
	rna-seq/Makefile

Log Message:
rna-seq: Meta-package for RNA-Seq differential gene expression

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=3bfdeb2c18878b9c19dcf2ca138d46bbca1035e9

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

diffstat:
 Makefile         |  1 +
 rna-seq/DESCR    | 11 +++++++++++
 rna-seq/Makefile | 25 +++++++++++++++++++++++++
 3 files changed, 37 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index efc2058f46..439e2c67c3 100644
--- a/Makefile
+++ b/Makefile
@@ -5093,6 +5093,7 @@ SUBDIR+=	rippled
 SUBDIR+=	rk
 SUBDIR+=	rlottie
 SUBDIR+=	rmilter
+SUBDIR+=	rna-seq
 SUBDIR+=	rnc-mode
 SUBDIR+=	rng-tools
 SUBDIR+=	rnp
diff --git a/rna-seq/DESCR b/rna-seq/DESCR
new file mode 100644
index 0000000000..5b792cc0aa
--- /dev/null
+++ b/rna-seq/DESCR
@@ -0,0 +1,11 @@
+The rna-seq meta-package provides the core tools needed for performing
+an RNA-Seq differential gene expression analysis, including adapter
+trimming, quality control, alignment, and identification of
+differentially expressed genes.  Researchers may want additional
+tools for data manipulation, gene ontology, etc.
+
+This package does not contain anything by itself -- it is a
+"meta-package" that depends on other packages.  Its sole purpose is
+to require dependencies so users can install this package only and
+have all the other packages pulled in by the package dependency
+mechanism.
diff --git a/rna-seq/Makefile b/rna-seq/Makefile
new file mode 100644
index 0000000000..c760b92fe2
--- /dev/null
+++ b/rna-seq/Makefile
@@ -0,0 +1,25 @@
+# $NetBSD$
+#
+
+DISTNAME=	rna-seq-1.0
+CATEGORIES=	meta-pkgs biology
+MASTER_SITES=	# empty
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+COMMENT=	Core tools needed for RNA-Seq analysis
+
+DEPENDS+=	fastq-trim>=0:../../wip/fastq-trim
+DEPENDS+=	fastqc>=0:../../biology/fastqc
+DEPENDS+=	biolibc-tools>=0:../../biology/biolibc-tools
+DEPENDS+=	gffread>=0:../../wip/gffread
+DEPENDS+=	kallisto>=0:../../biology/kallisto
+DEPENDS+=	bwa>=0:../../biology/bwa
+DEPENDS+=	bowtie2>=0:../../biology/bowtie2
+DEPENDS+=	hisat2>=0:../../biology/hisat2
+DEPENDS+=	igv>=0:../../biology/igv
+DEPENDS+=	samtools>=0:../../biology/samtools
+DEPENDS+=	fasda>=0:../../wip/fasda
+
+META_PACKAGE=	yes
+
+.include "../../mk/bsd.pkg.mk"