From nobody Wed Jan 11 23:47:29 2023 X-Original-To: dev-commits-ports-main@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 4Nskr13Vxwz2p4Nk; Wed, 11 Jan 2023 23:47:29 +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 4Nskr12lzbz451N; Wed, 11 Jan 2023 23:47:29 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1673480849; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=5hUct727uJsfB8ZG0lJ+iel8k/B0nQz/oiD4zrpiJLo=; b=XuFpSaPZ+UudhYDKY/eeuXgNePLoRFEvw5Bx0t1JFJNvl9E5MjRUjbz/iedBAEu/GoH08+ Gju8EX1IQmKaQbhI/ruH1+5h3w5P08QskbJsooytso5QNiJ3ZZpd6cUWcCNlhPEcNM88yK DwHCT560/9X/TvB0vLSyILW7VTaXd3U1/0zyvz2quGM+ysGSePyrcxc7SZahIa7PTi5SPI rEGPq2qesSo3r3oJU2T+iRCLWdmiRCL9bWOZuUgvTmGWXFKMzfQHIBwqg7KyFvk047D+Dl C/0wtTAScIsibdaCMxr1jsN7+PXKuERHnTzvBcPg+/G6+kov5OTZInlCSFUMcw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1673480849; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=5hUct727uJsfB8ZG0lJ+iel8k/B0nQz/oiD4zrpiJLo=; b=XEYM+osFijHoxhIIv3aUs1Qdey2Iv6c80O6inGxC+8R2/dAEAtrzoMBshdtv5UryfIqJEb 5muhBOrzdaqg6919ttzWeQErks39ZS0B20Mg4LyxvSc6E285dU7zqn/qH+gekN7MH6R8/t Hj8WKx34KsdjlzRs4Ir/ZLJ9eYb2+fMgcA9M+/5A5Z+ciEElSn9rMFjanUijUhilFeLk4l 80GOBDH1NGsg97rycAjE4EdbAvtMeO1D+rZJj1w6kIDU1W8553otvZgoeTubkzFNOZ4toe 2pj3o15ajOeQh6LrZwB1qCzRNbWT/jEnGGleHpe6YKicfkP+ZQMTaV/n0j3nZA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1673480849; a=rsa-sha256; cv=none; b=ntnnEdTGEyVXEGaSWucdH0XBAOeyMel2GJr6ADEcuojZ4/hzN5eZGKmh7bSPRq1M1gbhob w98vf4Y082QUqdp858Hnd5ZtFi68EAgIgFNAvJaBWhBu3fjgDK2M7K5eEgyaNoJD3TKmK9 LfhFci3/S+wXo2ftwAWRaDKjLx0I7t/Rk3hYqZB08JdUCqyKAkh9V5LanSX0OoJkWxjM0h Lfi3ZAMba1B/Czx98fHiaDiUgUQOwvTm6FETOnRK3MmrRY6DpO2sBhlNmQlRxnlEZneIbd aSzz/VYLIBxF2DMFpMBqjGr1Pusmx9uMFGxtn50l/GTUrDsOMDy7RExBaddrww== 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 4Nskr11p7kz16Dk; Wed, 11 Jan 2023 23:47:29 +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 30BNlTs4022840; Wed, 11 Jan 2023 23:47:29 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 30BNlTWk022839; Wed, 11 Jan 2023 23:47:29 GMT (envelope-from git) Date: Wed, 11 Jan 2023 23:47:29 GMT Message-Id: <202301112347.30BNlTWk022839@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: d2c13cc6fdc1 - main - biology/atac-seq: Metaport for ATAC-Seq analysis List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf commit d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf Author: Jason W. Bacon AuthorDate: 2023-01-11 23:47:02 +0000 Commit: Jason W. Bacon CommitDate: 2023-01-11 23:47:02 +0000 biology/atac-seq: Metaport for ATAC-Seq analysis Metaport to install tools for typical ATAC-Seq analysis, including QC, adapter trimming, alignment, and differential analysis. --- biology/Makefile | 1 + biology/atac-seq/Makefile | 27 +++++++++++++++++++++++++++ biology/atac-seq/distinfo | 1 + biology/atac-seq/pkg-descr | 2 ++ 4 files changed, 31 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 623fc167e24e..801bff937770 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -3,6 +3,7 @@ SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis + SUBDIR += atac-seq SUBDIR += augustus SUBDIR += avida SUBDIR += babel diff --git a/biology/atac-seq/Makefile b/biology/atac-seq/Makefile new file mode 100644 index 000000000000..6cc3e69e2535 --- /dev/null +++ b/biology/atac-seq/Makefile @@ -0,0 +1,27 @@ +PORTNAME= atac-seq +DISTVERSION= 0.1.0 +CATEGORIES= biology python +MASTER_SITES= # empty + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Metaport for ATAC-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/bowtie \ + samtools>0:biology/samtools \ + igv>0:biology/igv \ + ${PYTHON_PKGNAMEPREFIX}macs2>0:biology/py-macs2@${PY_FLAVOR} \ + fasda>0:biology/fasda \ + peak-classifier>0:biology/peak-classifier + +USES= metaport python + +.include diff --git a/biology/atac-seq/distinfo b/biology/atac-seq/distinfo new file mode 100644 index 000000000000..8bf439ee9d9b --- /dev/null +++ b/biology/atac-seq/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1673480732 diff --git a/biology/atac-seq/pkg-descr b/biology/atac-seq/pkg-descr new file mode 100644 index 000000000000..f4f9cd5c1975 --- /dev/null +++ b/biology/atac-seq/pkg-descr @@ -0,0 +1,2 @@ +Metaport to install tools for typical ATAC-Seq analysis, including QC, +adapter trimming, alignment, and differential analysis.