git: fddb1ea643a5 - main - biology/chip-seq: Metaport for ChIP-Seq analysis
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Date: Wed, 14 Jun 2023 21:23:38 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=fddb1ea643a59874932554e27ec62432a65aa136
commit fddb1ea643a59874932554e27ec62432a65aa136
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-06-14 21:22:35 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-06-14 21:23:37 +0000
biology/chip-seq: Metaport for ChIP-Seq analysis
Metaport to install tools for typical ChIP-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
Presently identical to biology/atac-seq, but may diverge in the future.
---
biology/Makefile | 1 +
biology/chip-seq/Makefile | 27 +++++++++++++++++++++++++++
biology/chip-seq/distinfo | 1 +
biology/chip-seq/pkg-descr | 2 ++
4 files changed, 31 insertions(+)
diff --git a/biology/Makefile b/biology/Makefile
index 927e88c08f00..c8654fab2077 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -32,6 +32,7 @@
SUBDIR += cd-hit
SUBDIR += cdbfasta
SUBDIR += checkm
+ SUBDIR += chip-seq
SUBDIR += clustal-omega
SUBDIR += clustalw
SUBDIR += cufflinks
diff --git a/biology/chip-seq/Makefile b/biology/chip-seq/Makefile
new file mode 100644
index 000000000000..5714a40951dd
--- /dev/null
+++ b/biology/chip-seq/Makefile
@@ -0,0 +1,27 @@
+PORTNAME= chip-seq
+DISTVERSION= 0.1.2
+CATEGORIES= biology python
+MASTER_SITES= # empty
+
+MAINTAINER= jwb@FreeBSD.org
+COMMENT= Metaport for ChIP-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/bowtie2 \
+ samtools>0:biology/samtools \
+ ${PYTHON_PKGNAMEPREFIX}macs2>0:biology/py-macs2@${PY_FLAVOR} \
+ fasda>0:biology/fasda \
+ peak-classifier>0:biology/peak-classifier \
+ webbrowser>0:www/webbrowser
+
+USES= metaport python
+
+.include <bsd.port.mk>
diff --git a/biology/chip-seq/distinfo b/biology/chip-seq/distinfo
new file mode 100644
index 000000000000..5912638d4af3
--- /dev/null
+++ b/biology/chip-seq/distinfo
@@ -0,0 +1 @@
+TIMESTAMP = 1686777697
diff --git a/biology/chip-seq/pkg-descr b/biology/chip-seq/pkg-descr
new file mode 100644
index 000000000000..d0bdf18d2c71
--- /dev/null
+++ b/biology/chip-seq/pkg-descr
@@ -0,0 +1,2 @@
+Metaport to install tools for typical ChIP-Seq analysis, including QC,
+adapter trimming, alignment, and differential analysis.