From nobody Mon Dec 12 17:30:01 2022 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 4NW7tL1xQ8z4kqtk; Mon, 12 Dec 2022 17:30:02 +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 4NW7tL0rwtz3hwK; Mon, 12 Dec 2022 17:30:02 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1670866202; 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=JCqZQPGZnwcZIAWtoDjHtPmGVg5SizxvJoDaGfoxr9k=; b=sqgI9zzyXQ9cTp7qQINXA5TfzW3HKPQPGG1X9oL98Wb3i8GAjEZbUX+eK08Cj/0/vlwoXo pJsXWNhpa4lJb+zV2UA2Kbz4iY4Cg0tRknJmgLTx/yjjZLLVZgoL2RQYdJ4u7o8486n+Nz M6438v9RqCi3nJkgWOGoGGkMcvB/i/2HrbU2uZJYYZzrLOb+e7AM7cX/X0hRtcTCJZsnai 9dSc/sSzYYeBEPftgPTyhrHz9BwrT+7n7k+bzQxonfce5FW/Cax2ED8LAiaz9v+TwDk9t3 +tQD5I+mYSIVk8Pst87OY/w6qCeJYajBXgL9KkxQGMV3tOxQbb/n4CgYWthp9Q== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1670866202; 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=JCqZQPGZnwcZIAWtoDjHtPmGVg5SizxvJoDaGfoxr9k=; b=GB0LxbepRnee+wfuv8qUuJT43Mj7Q3w157w0JB95oh9GgQBHi6vWqJjTgzbyW5Il8963Fu fDdCHNVKpJiIK1jHIRARrLGtzDb7W825q2cIBMftmXTHWnr2mtfJ6fOrQA8D+MoTqNQwHF 5hLNsRn2ZtlaJE4GA3th59u9kr/c2nc9hpZMSjqgh2XPtDbhX+Ic3JN5wVgEDGqc+j5ULr roWYH262tolmdRx+UjAsYfGiGNI17RZZKNGvkSmfEC+J44DExOZDed1LCFzrF0fyB+rhqp ORvA3qP3l07tVKKelWlTtYYWVkY0kFb8fGQ8CfmXZa8IdfcDAbxjf/0BtmEzFQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1670866202; a=rsa-sha256; cv=none; b=oAnKCLneUsn5mm4z1hPscy5gH1FT+0eL5EESbAY/if5+RBxLCGPfv7JE5wcR8uInR4laIo QiodhHlAAZ1F92gUWuwkvYZoM98iSpgAg9mgS/rOH5NLmyQBDfYtyGG8H44GQjfDRt8afR S9LVp5GW8weh5g4PGHsEHVTBn0MC5M7VFvViuDhj+x+hGPl5AmCORw0S80Go6a7vbXtH48 DT4F4Rbxjg8eYWSTcA64Dh49qtJtUXCn8iA+6lO0ZJtDJSrjf638vuX51WZ07DnY5euZNB mxbHUzNGE+PvLvU9O+7XfqEL4k1yKPaGxhjJ7fU47jpweezjPo021XZd+73MiQ== 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 4NW7tK6vznzhpN; Mon, 12 Dec 2022 17:30:01 +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 2BCHU1Dn017739; Mon, 12 Dec 2022 17:30:01 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2BCHU1Lw017735; Mon, 12 Dec 2022 17:30:01 GMT (envelope-from git) Date: Mon, 12 Dec 2022 17:30:01 GMT Message-Id: <202212121730.2BCHU1Lw017735@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: 8e926be18e0a - main - biology/rna-seq: Metaport for RNA-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: 8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22 commit 8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22 Author: Jason W. Bacon AuthorDate: 2022-12-12 17:29:36 +0000 Commit: Jason W. Bacon CommitDate: 2022-12-12 17:30:00 +0000 biology/rna-seq: Metaport for RNA-Seq analysis Metaport to install tools for typical RNA-Seq analysis, including QC, adapter trimming, alignment, and differential analysis. --- biology/Makefile | 1 + biology/rna-seq/Makefile | 26 ++++++++++++++++++++++++++ biology/rna-seq/distinfo | 1 + biology/rna-seq/pkg-descr | 2 ++ 4 files changed, 30 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index b544cbf16e59..b466435210cf 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -190,6 +190,7 @@ SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine + SUBDIR += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables diff --git a/biology/rna-seq/Makefile b/biology/rna-seq/Makefile new file mode 100644 index 000000000000..bdba35652327 --- /dev/null +++ b/biology/rna-seq/Makefile @@ -0,0 +1,26 @@ +PORTNAME= rna-seq +DISTVERSION= 0.1.0 +CATEGORIES= biology python +MASTER_SITES= # empty + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Metaport for RNA-Seq analysis +WWW= https://example.com/rna-seq + +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 \ + gffread>0:biology/gffread \ + kallisto>0:biology/kallisto \ + hisat2>0:biology/hisat2 \ + samtools>0:biology/samtools \ + igv>0:biology/igv \ + fasda>0:biology/fasda + +USES= metaport python + +.include diff --git a/biology/rna-seq/distinfo b/biology/rna-seq/distinfo new file mode 100644 index 000000000000..46e828c40768 --- /dev/null +++ b/biology/rna-seq/distinfo @@ -0,0 +1 @@ +TIMESTAMP = 1665354692 diff --git a/biology/rna-seq/pkg-descr b/biology/rna-seq/pkg-descr new file mode 100644 index 000000000000..f6986df491fc --- /dev/null +++ b/biology/rna-seq/pkg-descr @@ -0,0 +1,2 @@ +Metaport to install tools for typical RNA-Seq analysis, including QC, +adapter trimming, alignment, and differential analysis.