From nobody Thu Jan 16 12:41:19 2025 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 4YYjCg2pHhz5kPFS; Thu, 16 Jan 2025 12:41:19 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YYjCg228qz41lv; Thu, 16 Jan 2025 12:41:19 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737031279; 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=KUnXNcyLUOTiwn/N8fPEl73BPP6LsOr529Fjieet1os=; b=H+d3CWRPF6Oi4WjuGvK1UIuwXXntnost4gpF/aOoaUBro93Bj5lnZ5BKbX5+/QPNm1ldfP Qi04ktcB0NLLhLZ7Ado1zplERX/li6YH/I2LZoG2fv6C+cRj7UMrzz/ZCxEPfdYG115dCS nFDK1h7fA8HMyCDVr723zTMAgnPwJEwKOpy/Zt2NLCZ+lTAiVDG8MiMyI0S5LTupAZYysk 4VheSxPD65qU12i9WQ+hvzn2GI+cUaLV1VkzvO4g9/3JpAwnOpp70WA59zy0ESYkCj8EEX AOGP2Y4Y1E0JOL2JlP7cFCQaBN0C9lsyPdccw0c0tA8RPpAClHVoxgC0atDe4g== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737031279; 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=KUnXNcyLUOTiwn/N8fPEl73BPP6LsOr529Fjieet1os=; b=Is/iAGnlDwUOkyVlmUEp7xanunREsw9Af9rW1ADjaasmblmaylPCD5ECd4uU2x3P04AsoB GrLkhTZzBkw9lHUJ64lDrt47L+twWEWuG0zfOoZuQuIqLr7Sp1o9cPNfb62wQ/qjxxBOBP 1qL2rzD481V/9lkhELZaw1SHdNiVkgpcWf3+iJGbyVuV8tDuc76aLPkHlKQjVH7W4yBOAu XvnpnzlCjCdWEFjZ+3KFAEkSLqZ8jAiBiI3wUZdPwdPMVXaF8LmzldrS5Npr+09yc3Uz9q uMWxOlQI7/t+YZXUH5YNQFDCRQQbKKRXWtD/4tlk5sXpK5hTYQzBMBW1S7KxxQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1737031279; a=rsa-sha256; cv=none; b=j3DHOLEMxNmZx3bZlOkF/CSzUYlfHQ7QTeDDuC2APAyTCfLsqaLeWUYwGQSbn4keCmlYQg 2v+4j+AH8o9Tl+UnohUWUjBXvzRuqdj/dc2cucUgiaeDftjACfdTTX2KmfJ28m2Ln/LPly dVaNaVfooLZcZO7d8HOXfjAzGLVAWApDF93JCtZIrq/FQlc+E0pH6t8VtG+kTjOfipNTCL Ju7f6Ya+Rz6pPj20HDEikZgwb/jPotDPV6kiLZhQ+r/GAoTd6qzSOqvtI0f9lTHncp0wem 2Z/z6FCsv8oY+aFf6tvjXIgIyJPLaNnAyzzIPFNxdv5PZaJVIaI5OCFSjUTa8w== 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 4YYjCg1XxxzXcb; Thu, 16 Jan 2025 12:41:19 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 50GCfJud084479; Thu, 16 Jan 2025 12:41:19 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50GCfJZn084476; Thu, 16 Jan 2025 12:41:19 GMT (envelope-from git) Date: Thu, 16 Jan 2025 12:41:19 GMT Message-Id: <202501161241.50GCfJZn084476@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: 25e2eac767b4 - main - biology/bbmap: Update to 39.15 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-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: 25e2eac767b4fbfe69d5307fc027c5cfb8f44b77 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=25e2eac767b4fbfe69d5307fc027c5cfb8f44b77 commit 25e2eac767b4fbfe69d5307fc027c5cfb8f44b77 Author: Jason W. Bacon AuthorDate: 2025-01-16 12:35:49 +0000 Commit: Jason W. Bacon CommitDate: 2025-01-16 12:35:49 +0000 biology/bbmap: Update to 39.15 Add bitbucket link to WWW for some level of change tracking Release highlights: https://bitbucket.org/berkeleylab/jgi-bbtools/commits/branch/master Reported by: portscout --- biology/bbmap/Makefile | 5 +++-- biology/bbmap/distinfo | 6 +++--- biology/bbmap/pkg-plist | 10 ++++++++++ 3 files changed, 16 insertions(+), 5 deletions(-) diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index 7eb55b35a9e3..f9adfeb4db4f 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 39.14 +DISTVERSION= 39.15 CATEGORIES= biology java MASTER_SITES= SF/bbmap/ DISTNAME= BBMap_${PORTVERSION} @@ -7,7 +7,8 @@ DISTNAME= BBMap_${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= BBMap short read aligner, and other bioinformatic tools WWW= https://jgi.doe.gov/data-and-tools/bbtools/ \ - https://sourceforge.net/projects/bbmap/ + https://sourceforge.net/projects/bbmap/ \ + https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index c2f5a721063f..1bec09ddc1f9 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1736804942 -SHA256 (BBMap_39.14.tar.gz) = 87f7746dee28629afb368530457e7d2dfaabb4f8c5967dba4269d9a724f78e30 -SIZE (BBMap_39.14.tar.gz) = 12469315 +TIMESTAMP = 1737030117 +SHA256 (BBMap_39.15.tar.gz) = b6698469a2a90f4930537c575ff1f70332f88a933dd5e286c83ea0ff30802344 +SIZE (BBMap_39.15.tar.gz) = 12498916 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index d67fce64164a..1515769118ae 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -533,11 +533,21 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/bin/Cluster.java %%JAVAJARDIR%%/bbmap/bin/Contig.class %%JAVAJARDIR%%/bbmap/bin/Contig.java +%%JAVAJARDIR%%/bbmap/bin/ContigRenamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/ContigRenamer$Scaf.class +%%JAVAJARDIR%%/bbmap/bin/ContigRenamer.class +%%JAVAJARDIR%%/bbmap/bin/ContigRenamer.java %%JAVAJARDIR%%/bbmap/bin/DataLoader.class %%JAVAJARDIR%%/bbmap/bin/DataLoader.java +%%JAVAJARDIR%%/bbmap/bin/FileRenamer.class +%%JAVAJARDIR%%/bbmap/bin/FileRenamer.java %%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.java +%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG$Genome.class +%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG.class +%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG.java %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.class %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.java %%JAVAJARDIR%%/bbmap/bin/SketchRecord.class