git: 799d4cc2cfd1 - main - biology/py-deeptools: User-friendly tools for exploring deep-sequencing data

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=799d4cc2cfd1c343f486afbde5cc735ec206de2e

commit 799d4cc2cfd1c343f486afbde5cc735ec206de2e
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2021-10-14 11:51:12 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2021-10-14 11:51:12 +0000

    biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
    
    deepTools contains useful modules to process the mapped reads data for
    multiple quality checks, creating normalized coverage files in standard
    bedGraph and bigWig file formats, that allow comparison between
    different files (for example, treatment and control). Finally, using
    such normalized and standardized files, deepTools can create many
    publication-ready visualizations to identify enrichments and for
    functional annotations of the genome.
---
 biology/Makefile               |  1 +
 biology/py-deeptools/Makefile  | 26 ++++++++++++++++++++++++++
 biology/py-deeptools/distinfo  |  3 +++
 biology/py-deeptools/pkg-descr |  9 +++++++++
 4 files changed, 39 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index a49bdebebeef..c4fd2890bcf3 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -144,6 +144,7 @@
     SUBDIR += py-bx-python
     SUBDIR += py-crossmap
     SUBDIR += py-cutadapt
+    SUBDIR += py-deeptools
     SUBDIR += py-deeptoolsintervals
     SUBDIR += py-dnaio
     SUBDIR += py-ete3
diff --git a/biology/py-deeptools/Makefile b/biology/py-deeptools/Makefile
new file mode 100644
index 000000000000..fb7dd40ad021
--- /dev/null
+++ b/biology/py-deeptools/Makefile
@@ -0,0 +1,26 @@
+PORTNAME=	deepTools
+DISTVERSION=	3.5.1
+CATEGORIES=	biology python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	User-friendly tools for exploring deep-sequencing data
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+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} \
+		${PYTHON_PKGNAMEPREFIX}pysam>=0.14.0:biology/py-pysam@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}py2bit>=0.3.0:biology/py-py2bit@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpydoc>=0.5:textproc/py-numpydoc@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pyBigWig>=0.3.18:biology/py-pybigwig@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}plotly>=4.9:graphics/py-plotly@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}deeptoolsintervals>=0.1.8:biology/py-deeptoolsintervals@${PY_FLAVOR}
+
+USES=		python
+USE_PYTHON=	autoplist concurrent distutils
+
+.include <bsd.port.mk>
diff --git a/biology/py-deeptools/distinfo b/biology/py-deeptools/distinfo
new file mode 100644
index 000000000000..8e524e070d7b
--- /dev/null
+++ b/biology/py-deeptools/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1617285775
+SHA256 (deepTools-3.5.1.tar.gz) = 62eea132513afa5f6bb51387e5866a5c3a26613aeb7e8c9600c38becf2ecb716
+SIZE (deepTools-3.5.1.tar.gz) = 199732
diff --git a/biology/py-deeptools/pkg-descr b/biology/py-deeptools/pkg-descr
new file mode 100644
index 000000000000..35d810a014b3
--- /dev/null
+++ b/biology/py-deeptools/pkg-descr
@@ -0,0 +1,9 @@
+deepTools contains useful modules to process the mapped reads data for
+multiple quality checks, creating normalized coverage files in standard
+bedGraph and bigWig file formats, that allow comparison between
+different files (for example, treatment and control). Finally, using
+such normalized and standardized files, deepTools can create many
+publication-ready visualizations to identify enrichments and for
+functional annotations of the genome.
+
+WWW: https://github.com/deeptools/deepTools