git: d2c13cc6fdc1 - main - biology/atac-seq: Metaport for ATAC-Seq analysis

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf

commit d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-01-11 23:47:02 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-01-11 23:47:02 +0000

    biology/atac-seq: Metaport for ATAC-Seq analysis
    
    Metaport to install tools for typical ATAC-Seq analysis, including QC,
    adapter trimming, alignment, and differential analysis.
---
 biology/Makefile           |  1 +
 biology/atac-seq/Makefile  | 27 +++++++++++++++++++++++++++
 biology/atac-seq/distinfo  |  1 +
 biology/atac-seq/pkg-descr |  2 ++
 4 files changed, 31 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 623fc167e24e..801bff937770 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -3,6 +3,7 @@
     SUBDIR += abyss
     SUBDIR += ad2vcf
     SUBDIR += artemis
+    SUBDIR += atac-seq
     SUBDIR += augustus
     SUBDIR += avida
     SUBDIR += babel
diff --git a/biology/atac-seq/Makefile b/biology/atac-seq/Makefile
new file mode 100644
index 000000000000..6cc3e69e2535
--- /dev/null
+++ b/biology/atac-seq/Makefile
@@ -0,0 +1,27 @@
+PORTNAME=	atac-seq
+DISTVERSION=	0.1.0
+CATEGORIES=	biology python
+MASTER_SITES=	# empty
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Metaport for ATAC-Seq analysis
+WWW=		https://github.com/auerlab/
+
+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 \
+		bwa>0:biology/bwa \
+		bowtie2>0:biology/bowtie \
+		samtools>0:biology/samtools \
+		igv>0:biology/igv \
+		${PYTHON_PKGNAMEPREFIX}macs2>0:biology/py-macs2@${PY_FLAVOR} \
+		fasda>0:biology/fasda \
+		peak-classifier>0:biology/peak-classifier
+
+USES=		metaport python
+
+.include <bsd.port.mk>
diff --git a/biology/atac-seq/distinfo b/biology/atac-seq/distinfo
new file mode 100644
index 000000000000..8bf439ee9d9b
--- /dev/null
+++ b/biology/atac-seq/distinfo
@@ -0,0 +1 @@
+TIMESTAMP = 1673480732
diff --git a/biology/atac-seq/pkg-descr b/biology/atac-seq/pkg-descr
new file mode 100644
index 000000000000..f4f9cd5c1975
--- /dev/null
+++ b/biology/atac-seq/pkg-descr
@@ -0,0 +1,2 @@
+Metaport to install tools for typical ATAC-Seq analysis, including QC,
+adapter trimming, alignment, and differential analysis.