git: 8e926be18e0a - main - biology/rna-seq: Metaport for RNA-Seq analysis

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22

commit 8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-12-12 17:29:36 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-12-12 17:30:00 +0000

    biology/rna-seq: Metaport for RNA-Seq analysis
    
    Metaport to install tools for typical RNA-Seq analysis, including QC,
    adapter trimming, alignment, and differential analysis.
---
 biology/Makefile          |  1 +
 biology/rna-seq/Makefile  | 26 ++++++++++++++++++++++++++
 biology/rna-seq/distinfo  |  1 +
 biology/rna-seq/pkg-descr |  2 ++
 4 files changed, 30 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index b544cbf16e59..b466435210cf 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -190,6 +190,7 @@
     SUBDIR += rampler
     SUBDIR += readseq
     SUBDIR += recombine
+    SUBDIR += rna-seq
     SUBDIR += ruby-bio
     SUBDIR += rubygem-bio
     SUBDIR += rubygem-bio-executables
diff --git a/biology/rna-seq/Makefile b/biology/rna-seq/Makefile
new file mode 100644
index 000000000000..bdba35652327
--- /dev/null
+++ b/biology/rna-seq/Makefile
@@ -0,0 +1,26 @@
+PORTNAME=	rna-seq
+DISTVERSION=	0.1.0
+CATEGORIES=	biology python
+MASTER_SITES=	# empty
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Metaport for RNA-Seq analysis
+WWW=		https://example.com/rna-seq
+
+LICENSE=	BSD2CLAUSE
+
+RUN_DEPENDS=	sra-tools>0:biology/sra-tools \
+		fastq-trim>0:biology/fastq-trim \
+		fastqc>0:biology/fastqc \
+		${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR} \
+		biolibc-tools>0:biology/biolibc-tools \
+		gffread>0:biology/gffread \
+		kallisto>0:biology/kallisto \
+		hisat2>0:biology/hisat2 \
+		samtools>0:biology/samtools \
+		igv>0:biology/igv \
+		fasda>0:biology/fasda
+
+USES=		metaport python
+
+.include <bsd.port.mk>
diff --git a/biology/rna-seq/distinfo b/biology/rna-seq/distinfo
new file mode 100644
index 000000000000..46e828c40768
--- /dev/null
+++ b/biology/rna-seq/distinfo
@@ -0,0 +1 @@
+TIMESTAMP = 1665354692
diff --git a/biology/rna-seq/pkg-descr b/biology/rna-seq/pkg-descr
new file mode 100644
index 000000000000..f6986df491fc
--- /dev/null
+++ b/biology/rna-seq/pkg-descr
@@ -0,0 +1,2 @@
+Metaport to install tools for typical RNA-Seq analysis, including QC,
+adapter trimming, alignment, and differential analysis.