From nobody Fri Aug 11 20:44:47 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 4RMwlM6Xnwz4mRZx; Fri, 11 Aug 2023 20:44:47 +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 4RMwlM5KmNz3Vcp; Fri, 11 Aug 2023 20:44:47 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691786687; 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=J1xhpDl3jatnC32cLCCdSp4KdglSWnFvWxplQBu2Oqw=; b=vHP4Bcw6LtAs0R/mp+nIaj26IAtPVTnDtZ3mXor1Io/5b0vpgb51SJERmj63zfKPnrXs24 5y1yynJqA7S9VNhhC6hIkkxMT+RdobMC3Dcpaxl6jipLLuAGOddatZrY2yedhcDDigc9ll CIIJpA7EYPzOZXYO/NLUQ7UCLR72iRPh3xLAmeIDstYj+l7B+wSF26EjVAr5A8tRmL/qzn aPP4bfzWPFl02o923T4J294FtY6DpdveiefsgEH49GOJA8ZEDwXy8pFM0hNs2D/pgVKA5h ged+3vrOJxdwvvf3ffzmLngWIraTCzWJhX7ghdz/woJfPSw8JGnxpuq8pp9vlQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691786687; 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=J1xhpDl3jatnC32cLCCdSp4KdglSWnFvWxplQBu2Oqw=; b=uD+3jgWGb4X83V1ljdtrS0tleeSLmEA3xMRGgJrb38Pr3UWkina3gDLAIgQUSLDWKVj2lq XbA4zvbbTNbAAL6j9z7BAXqfAykFWvmNaPvVstzbBpXbXST0v7WsdRV9ubkhziDu0/JLom /3Bypv0kn0sXP2fl6AgsRK14updeejcYOieRf7A0zj50QBU14d7YsOIbrKC6HDjCPjUoAE YScBwVo4wDw4Wy6FrEjfZJvmX2ej7HZYpSsdr3Eh0A0pjmcV3fMkdnstEeUy0W/hOtXAk6 5UYqG7sJE6g7krjguh8ror/Jkb20d6B2vg8DZ4JOnz74kdgHVhidFuKFhBeSMA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1691786687; a=rsa-sha256; cv=none; b=HOlskBXnQ/Xbi40CDlFYTFaTCM3rq/Vo1/vYJEMuqJRW7dSWL8uzAQZACW/jbfdRvQaw6m wVutPEeHEh12Pkgl2O8eu0FiLgGBN69IyknAn1jY2VDNeN/M6t47gZ9ekf3m9QGbjRLI+A LkTK0yWyP3cH72vrqNUd+HE1UgER4+woPrRZSdxhToS8c0W/lmO2pnYAQ3TRxC04ldLulJ /ohXrpHSKqweXCNB7Xx5+TBsGRf3z9suhgeRlfTXz+vz9CBLfslTdUYfS8g2ox4E5AKBTK XE2eMVn6u0kbhqHOI5sob9wRwC8Z8a95+qhETOUNBg0pRCZUheoSOH442imY9w== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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 4RMwlM4RWZztGS; Fri, 11 Aug 2023 20:44:47 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 37BKilMx055176; Fri, 11 Aug 2023 20:44:47 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 37BKilMC055173; Fri, 11 Aug 2023 20:44:47 GMT (envelope-from git) Date: Fri, 11 Aug 2023 20:44:47 GMT Message-Id: <202308112044.37BKilMC055173@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: 67773b0db360 - main - biology/fasda: Update to 0.1.4 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: 67773b0db360dbd23843d82d0d63ba78da9e9457 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=67773b0db360dbd23843d82d0d63ba78da9e9457 commit 67773b0db360dbd23843d82d0d63ba78da9e9457 Author: Jason W. Bacon AuthorDate: 2023-08-11 20:39:06 +0000 Commit: Jason W. Bacon CommitDate: 2023-08-11 20:39:06 +0000 biology/fasda: Update to 0.1.4 Add --debug Replace --map-gene with --feature-type for more flexibility Use extended REs for gff3 feature selection (default = RNA$|transcript$|gene_segment$, same as transcript in GTF) Add --output-dir Support |-separated ID aliases (report last alias) Support outsourcing abundance calculation (default = stringtie) Several bug fixes and minor enhancements Changes: https://github.com/auerlab/fasda/releases --- biology/fasda/Makefile | 3 ++- biology/fasda/distinfo | 6 +++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/biology/fasda/Makefile b/biology/fasda/Makefile index e7dc7ed5a3a7..3c9823658748 100644 --- a/biology/fasda/Makefile +++ b/biology/fasda/Makefile @@ -1,5 +1,5 @@ PORTNAME= fasda -DISTVERSION= 0.1.3 +DISTVERSION= 0.1.4 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -10,6 +10,7 @@ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libxtend.so:devel/libxtend libbiolibc.so:biology/biolibc +RUN_DEPENDS= stringtie>0:biology/stringtie USES= localbase USE_GITHUB= yes diff --git a/biology/fasda/distinfo b/biology/fasda/distinfo index 388673460271..88743d780fa6 100644 --- a/biology/fasda/distinfo +++ b/biology/fasda/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1686347287 -SHA256 (auerlab-fasda-0.1.3_GH0.tar.gz) = 1e1fb36327b63c53cd4286dbd6edfd89cf2bdc0899fe8d8b748b01fbb1d91d47 -SIZE (auerlab-fasda-0.1.3_GH0.tar.gz) = 59513 +TIMESTAMP = 1691756858 +SHA256 (auerlab-fasda-0.1.4_GH0.tar.gz) = 8e1b1536ff3c551c16b6ddca543378343e055a9b067ef5038e2b2f1fb2e874b9 +SIZE (auerlab-fasda-0.1.4_GH0.tar.gz) = 65254