From nobody Tue Dec 14 19:45:37 2021 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 CF50B18EA7DB; Tue, 14 Dec 2021 19:45:40 +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 4JD84L4mqDz4vjG; Tue, 14 Dec 2021 19:45:38 +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 0F64A698A; Tue, 14 Dec 2021 19:45:38 +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 1BEJjbm1035892; Tue, 14 Dec 2021 19:45:37 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1BEJjbaW035891; Tue, 14 Dec 2021 19:45:37 GMT (envelope-from git) Date: Tue, 14 Dec 2021 19:45:37 GMT Message-Id: <202112141945.1BEJjbaW035891@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: 3a7f92ec883e - main - biology/biolibc-tools: Update to 0.1.1 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: 3a7f92ec883e0d6926de8afe2e1c2ee8a005c13f Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1639511139; 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=/hbqAPF5jubwe1yxYZUYgSf4v+Wv8u6fyJrvDIsBD40=; b=N/kjnGvzwkShGcmqQ6ac/XPUNSgKmQ4GvRE29sdTMhF3L1Q3p91MXvdLbiYSTC7VvkPhad Dq5pmG/1ONOdqWybtLgNouK1F2IHpgZQpiA3zqttX3U3IqITFvDqKvt/ACkdshyIhRNsXE 3on+ACg9+J3/litEuj25hX2W/Rmaa/QRtlZemaOP8vo/eH76Sjjk7ZQAC8KjF22VGGC8NZ eSEynjMIhpl0YuGPiS7RBTcIlfj37cfZOWnKzQjtkHOjbE17L3gq627dXJjhAbjgwR9Z6E 4D4KYZYw05HYAHyzDGjpyCgedu/XKEHyFpfgIz4d3VLDabeGcjeV9rQz4L1oLA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1639511139; a=rsa-sha256; cv=none; b=DfS9JqQMjL6GrrfHMxOXs6pr3ANP4u2sUEBNgEV912ETnKC/+YRUzzNS70KroS+FynhGj0 aDtvFa+uigj8NpW7h4x0kRE6ZLyjjuBudSoc+npcprJtmJFxHmqb7vWwmLXRjFOynviFV+ 7i7aGq0omW49EgE8O6rMhq9BGRyF7R1ORbKAL8ogbudHJEQTQOCDxES8IRXoznooAOrLbC keL6U6pMDskm2rWucmKUkro0EWM1AEafgIAxekyuYeasIW3hyKwPYTb60Tiwd6gcbcldVk 0MyQWPSQVzmnI7PnHuV2hMZxcAlg+P3kf1DfpokmuG0ZxQ8wSTbGdckz/ExKeg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=3a7f92ec883e0d6926de8afe2e1c2ee8a005c13f commit 3a7f92ec883e0d6926de8afe2e1c2ee8a005c13f Author: Jason W. Bacon AuthorDate: 2021-12-14 19:42:10 +0000 Commit: Jason W. Bacon CommitDate: 2021-12-14 19:45:32 +0000 biology/biolibc-tools: Update to 0.1.1 Make all programs subcommands of "blt" Several new commands Updates for evolving libxtend and biolibc APIs Add --version flag Numerous minor fixes and enhancements Changes: https://github.com/auerlab/biolibc-tools/releases/tag/0.1.1 --- biology/biolibc-tools/Makefile | 5 ++--- biology/biolibc-tools/distinfo | 6 +++--- biology/biolibc-tools/pkg-plist | 26 ++++++++++++++++++++------ 3 files changed, 25 insertions(+), 12 deletions(-) diff --git a/biology/biolibc-tools/Makefile b/biology/biolibc-tools/Makefile index 39913d8b5347..4a63e3749e93 100644 --- a/biology/biolibc-tools/Makefile +++ b/biology/biolibc-tools/Makefile @@ -1,8 +1,7 @@ # Created by: J. Bacon PORTNAME= biolibc-tools -DISTVERSION= 0.1.0-34 -DISTVERSIONSUFFIX= -gf1224de +DISTVERSION= 0.1.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -13,13 +12,13 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= uthash>0:devel/uthash LIB_DEPENDS= libbiolibc.so:biology/biolibc \ - libxtend.so:devel/libxtend \ libxxhash.so:devel/xxhash USE_GITHUB= yes GH_ACCOUNT= auerlab +MAKE_ENV= VERSION=${PORTVERSION} INSTALL_TARGET= install-strip pre-build: diff --git a/biology/biolibc-tools/distinfo b/biology/biolibc-tools/distinfo index 9a1bab65b7ce..d3732ec6c333 100644 --- a/biology/biolibc-tools/distinfo +++ b/biology/biolibc-tools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1630328729 -SHA256 (auerlab-biolibc-tools-0.1.0-34-gf1224de_GH0.tar.gz) = c63309cad0e73a9336deebfc9ea9104320810d45631141ec1a8554f6cf5a6cf7 -SIZE (auerlab-biolibc-tools-0.1.0-34-gf1224de_GH0.tar.gz) = 11683 +TIMESTAMP = 1639495090 +SHA256 (auerlab-biolibc-tools-0.1.1_GH0.tar.gz) = 169ea4bbd70049d9e364e145db0ca4793da99202f12262e00485407cfbd2997b +SIZE (auerlab-biolibc-tools-0.1.1_GH0.tar.gz) = 21700 diff --git a/biology/biolibc-tools/pkg-plist b/biology/biolibc-tools/pkg-plist index 04756a2801be..f5fe188a60a8 100644 --- a/biology/biolibc-tools/pkg-plist +++ b/biology/biolibc-tools/pkg-plist @@ -1,7 +1,21 @@ -bin/fastq-derep.sh -bin/fastx-derep -bin/fastx2tsv +bin/blt +libexec/biolibc-tools/chrom-lens +libexec/biolibc-tools/extract-seq +libexec/biolibc-tools/fasta2seq +libexec/biolibc-tools/fastq-derep.sh +libexec/biolibc-tools/fastx-derep +libexec/biolibc-tools/fastx2tsv +libexec/biolibc-tools/find-orfs +libexec/biolibc-tools/gff2bed libexec/biolibc-tools/uniq-seqs.awk -man/man1/fastq-dedup.sh.1.gz -man/man1/fastx-derep.1.gz -man/man1/fastx2tsv.1.gz +libexec/biolibc-tools/vcf-search +man/man1/blt-chrom-lens.1.gz +man/man1/blt-extract-seq.1.gz +man/man1/blt-fasta2seq.1.gz +man/man1/blt-fastq-derep.sh.1.gz +man/man1/blt-fastx-derep.1.gz +man/man1/blt-fastx2tsv.1.gz +man/man1/blt-find-orfs.1.gz +man/man1/blt-gff2bed.1.gz +man/man1/blt-vcf-search.1.gz +man/man1/blt.1.gz