From owner-dev-commits-ports-all@freebsd.org Mon Jun 14 16:42:16 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 0E09D653A5E; Mon, 14 Jun 2021 16:42:16 +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 4G3cgC6hM9z3pBJ; Mon, 14 Jun 2021 16:42:15 +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 CCBDE184F1; Mon, 14 Jun 2021 16:42:15 +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 15EGgFcb069624; Mon, 14 Jun 2021 16:42:15 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 15EGgFn6069623; Mon, 14 Jun 2021 16:42:15 GMT (envelope-from git) Date: Mon, 14 Jun 2021 16:42:15 GMT Message-Id: <202106141642.15EGgFn6069623@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: 5a2a6eb32954 - main - biology/peak-classifier: Classify peaks based on GFF features 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: 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 14 Jun 2021 16:42:16 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5a2a6eb32954aa49c79269b08fd7e26ca4436f3d commit 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d Author: Jason W. Bacon AuthorDate: 2021-06-14 16:40:33 +0000 Commit: Jason W. Bacon CommitDate: 2021-06-14 16:40:33 +0000 biology/peak-classifier: Classify peaks based on GFF features Classify ChIP/ATAC-Seq peaks based on features provided in a GFF Peaks are provided in a BED file sorted by chromosome and position. The GFF must be sorted by chromosome and position, with gene-level features separated by ### tags and each gene organized into subfeatures such as transcripts and exons. This is the default for common data sources. --- biology/Makefile | 1 + biology/peak-classifier/Makefile | 24 ++++++++++++++++++++++++ biology/peak-classifier/distinfo | 3 +++ biology/peak-classifier/pkg-descr | 8 ++++++++ biology/peak-classifier/pkg-plist | 9 +++++++++ 5 files changed, 45 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 4025c269aef3..4acd54fab965 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -112,6 +112,7 @@ SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan + SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred diff --git a/biology/peak-classifier/Makefile b/biology/peak-classifier/Makefile new file mode 100644 index 000000000000..e964f1b7b49a --- /dev/null +++ b/biology/peak-classifier/Makefile @@ -0,0 +1,24 @@ +PORTNAME= peak-classifier +DISTVERSION= 0.1.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Classify ChIP/ATAC-Seq peaks based on features provided in a GFF + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libxtend.so:devel/libxtend libbiolibc.so:biology/biolibc +RUN_DEPENDS= bedtools:biology/bedtools \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} + +USES= localbase python:3.7+ shebangfix +USE_GITHUB= yes + +GH_ACCOUNT= auerlab +SHEBANG_FILES= feature-view.py + +pre-build: + cd ${WRKSRC} && make depend LOCALBASE=${LOCALBASE} + +.include diff --git a/biology/peak-classifier/distinfo b/biology/peak-classifier/distinfo new file mode 100644 index 000000000000..43f3d37e76fb --- /dev/null +++ b/biology/peak-classifier/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1623687381 +SHA256 (auerlab-peak-classifier-0.1.1_GH0.tar.gz) = 45230d50f204ecf1fa0f8bb1c96f00c25d84ae592b8def1cf053a07de60a8c7b +SIZE (auerlab-peak-classifier-0.1.1_GH0.tar.gz) = 86012 diff --git a/biology/peak-classifier/pkg-descr b/biology/peak-classifier/pkg-descr new file mode 100644 index 000000000000..b123dcbc554d --- /dev/null +++ b/biology/peak-classifier/pkg-descr @@ -0,0 +1,8 @@ +Classify ChIP/ATAC-Seq peaks based on features provided in a GFF + +Peaks are provided in a BED file sorted by chromosome and position. The GFF +must be sorted by chromosome and position, with gene-level features separated +by ### tags and each gene organized into subfeatures such as transcripts and +exons. This is the default for common data sources. + +WWW: https://github.com/auerlab/peak-classifier diff --git a/biology/peak-classifier/pkg-plist b/biology/peak-classifier/pkg-plist new file mode 100644 index 000000000000..787333471195 --- /dev/null +++ b/biology/peak-classifier/pkg-plist @@ -0,0 +1,9 @@ +bin/extract-genes +bin/feature-view +bin/filter-overlaps +bin/peak-classifier +libexec/extract-genes.awk +man/man1/extract-genes.1.gz +man/man1/feature-view.1.gz +man/man1/filter-overlaps.1.gz +man/man1/peak-classifier.1.gz