diff --git a/biology/py-deeptools/Makefile b/biology/py-deeptools/Makefile
index e83d82db1e00..64cda435743f 100644
--- a/biology/py-deeptools/Makefile
+++ b/biology/py-deeptools/Makefile
@@ -1,28 +1,32 @@
 PORTNAME=	deepTools
-DISTVERSION=	3.5.2
-PORTREVISION=	3
+DISTVERSION=	3.5.6
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+DISTNAME=	deeptools-${DISTVERSION}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	User-friendly tools for exploring deep-sequencing data
 WWW=		https://github.com/deeptools/deepTools
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools>0:devel/py-setuptools@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
+RUN_DEPENDS=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}scipy>=0.17.0:science/py-scipy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>=3.5.0:math/py-matplotlib@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pysam>=0.14.0:biology/py-pysam@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}py2bit>=0.3.0:biology/py-py2bit@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}py2bit>=0.2.0:biology/py-py2bit@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}numpydoc>=0.5:textproc/py-numpydoc@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pyBigWig>=0.3.18:biology/py-pybigwig@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pyBigWig>=0.2.1:biology/py-pybigwig@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}plotly>=4.9:graphics/py-plotly@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}deeptoolsintervals>=0.1.8:biology/py-deeptoolsintervals@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	autoplist concurrent distutils
+USE_PYTHON=	autoplist concurrent pep517
+
+NO_ARCH=	yes
 
 .include <bsd.port.mk>
diff --git a/biology/py-deeptools/distinfo b/biology/py-deeptools/distinfo
index d9f91ee6f45e..7bfa323c9994 100644
--- a/biology/py-deeptools/distinfo
+++ b/biology/py-deeptools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1687035894
-SHA256 (deepTools-3.5.2.tar.gz) = 9367f9037b1822b7d69d5abaf47ca25bf0e5dc4cb8be85bd55b6f63c90781941
-SIZE (deepTools-3.5.2.tar.gz) = 203152
+TIMESTAMP = 1777290929
+SHA256 (deeptools-3.5.6.tar.gz) = 2daf06abc8cf2df42f7e0ecacb3784ee95de1db4dd887f69f22a29f27e202369
+SIZE (deeptools-3.5.6.tar.gz) = 199316