From owner-dev-commits-ports-main@freebsd.org Wed May 26 22:25:24 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id C7472647E53; Wed, 26 May 2021 22:25:24 +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 4Fr59w5Ctsz4v49; Wed, 26 May 2021 22:25:24 +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 9131419112; Wed, 26 May 2021 22:25:24 +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 14QMPOOE001212; Wed, 26 May 2021 22:25:24 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 14QMPOVR001211; Wed, 26 May 2021 22:25:24 GMT (envelope-from git) Date: Wed, 26 May 2021 22:25:24 GMT Message-Id: <202105262225.14QMPOVR001211@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: be2fb2f2905d - main - biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set operations on k-mers MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: be2fb2f2905d13d5f2463688dbf319f5940cfccc Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 26 May 2021 22:25:24 -0000 The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=be2fb2f2905d13d5f2463688dbf319f5940cfccc commit be2fb2f2905d13d5f2463688dbf319f5940cfccc Author: Yuri Victorovich AuthorDate: 2021-05-26 21:39:02 +0000 Commit: Yuri Victorovich CommitDate: 2021-05-26 22:25:21 +0000 biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set operations on k-mers --- biology/Makefile | 1 + biology/unikmer/Makefile | 19 +++++++++++++++++++ biology/unikmer/distinfo | 5 +++++ biology/unikmer/pkg-descr | 12 ++++++++++++ 4 files changed, 37 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index e5bec235ca01..38761df9c785 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -185,6 +185,7 @@ SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene + SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile new file mode 100644 index 000000000000..fa7eec68c77b --- /dev/null +++ b/biology/unikmer/Makefile @@ -0,0 +1,19 @@ +PORTNAME= unikmer +DISTVERSIONPREFIX= v +DISTVERSION= 0.18.0 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Toolkit for nucleic acid k-mer analysis, set operations on k-mers + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= go:modules + +GO_MODULE= github.com/shenwei356/unikmer +GO_TARGET= ./${PORTNAME} + +PLIST_FILES= bin/${PORTNAME} + +.include diff --git a/biology/unikmer/distinfo b/biology/unikmer/distinfo new file mode 100644 index 000000000000..934330ac60cd --- /dev/null +++ b/biology/unikmer/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1622064837 +SHA256 (go/biology_unikmer/unikmer-v0.18.0/v0.18.0.mod) = 6ccade17e0fdfc86ebaa0683f7aab4e3c94019032e0d0f4c78bf957a2a8f9c1b +SIZE (go/biology_unikmer/unikmer-v0.18.0/v0.18.0.mod) = 881 +SHA256 (go/biology_unikmer/unikmer-v0.18.0/v0.18.0.zip) = ff1d28fc6c79d62fc1a240bec03acc604f9ef7375f22548e0cc472c41b5b349d +SIZE (go/biology_unikmer/unikmer-v0.18.0/v0.18.0.zip) = 4273162 diff --git a/biology/unikmer/pkg-descr b/biology/unikmer/pkg-descr new file mode 100644 index 000000000000..7ae41bf53489 --- /dev/null +++ b/biology/unikmer/pkg-descr @@ -0,0 +1,12 @@ +unikmer is a golang package and a toolkit for nucleic acid k-mer analysis, +providing functions including set operation k-mers (sketch) optional with TaxIds +but without count information. + +K-mers are either encoded (k<=32) or hashed (arbitrary k) into uint64, and +serialized in binary file with extension .unik. + +TaxIds can be assigned when counting k-mers from genome sequences, and LCA +(Lowest Common Ancestor) is computed during set opertions including computing +union, intersecton, set difference, unique and repeated k-mers. + +WWW: https://github.com/shenwei356/unikmer