From nobody Thu Oct 14 11:54:09 2021 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 0032D18149BA; Thu, 14 Oct 2021 11:54:10 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4HVSVT6f84z4hjY; Thu, 14 Oct 2021 11:54:09 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id C3CD312B7D; Thu, 14 Oct 2021 11:54:09 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 19EBs9rB000944; Thu, 14 Oct 2021 11:54:09 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 19EBs96k000943; Thu, 14 Oct 2021 11:54:09 GMT (envelope-from git) Date: Thu, 14 Oct 2021 11:54:09 GMT Message-Id: <202110141154.19EBs96k000943@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 799d4cc2cfd1 - main - biology/py-deeptools: User-friendly tools for exploring deep-sequencing data List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 799d4cc2cfd1c343f486afbde5cc735ec206de2e Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=799d4cc2cfd1c343f486afbde5cc735ec206de2e commit 799d4cc2cfd1c343f486afbde5cc735ec206de2e Author: Jason W. Bacon AuthorDate: 2021-10-14 11:51:12 +0000 Commit: Jason W. Bacon 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 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