From nobody Sun Dec 05 20:50:57 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 9012D18BCF18; Sun, 5 Dec 2021 20:50:57 +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 4J6dxs1mVSz3FBv; Sun, 5 Dec 2021 20:50:57 +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 1C9151EBC4; Sun, 5 Dec 2021 20:50:57 +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 1B5Kovcs001559; Sun, 5 Dec 2021 20:50:57 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1B5KovZ3001558; Sun, 5 Dec 2021 20:50:57 GMT (envelope-from git) Date: Sun, 5 Dec 2021 20:50:57 GMT Message-Id: <202112052050.1B5KovZ3001558@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: 864d4fdd1804 - main - biology/libgff: GFF/GTF parsing library based on GCLib 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: 864d4fdd1804d2d4f46619f781e397b9ccdf1639 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1638737457; 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=CsrEnbqUh5cFy6oVMyQQ+dICXP9SR2+LHpzd7HWNIng=; b=vcfuX8l8t28uTB/1AZ9I6+YJpV2eGm7VpkQ788TXIrrJjxiODpA9pqZ5bBG/lEVmS2pACu daXRBtAbACzD6cxKPxXxCEOdksYPEQP9HLMsACR4GKFDEHSKVXxmFKz2/+lsDsgxbHPaxy oWB6JS+xkZO95MT9WYBgUWeKHk5huRApkruI/9eRV3pa0mRq30JJSMktQ/7UzZ9bO71rhp jKTOCNdLBxxcmdxlv2ybpFyq04dMgAGU0Ndxs2ygcldwoPpzIr55rnDSYNolX44rDyxVlu kTYfKrsZfiVYTw4auRc4KIOaAtGcwUxtnDBqW+n1wF0EqI+Isp5ACIrmeSfGNA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1638737457; a=rsa-sha256; cv=none; b=dlX/8xDls0tJN8O71Gtbn8//QkgYLK7HeoABfbW9/Yh5KPKyhZd00yvwVShPZA9RYdZO7g 7gkNvDmSIQRDE6rSF3H8hW2fWTovLqO2fIBiFcBJyWwYv1PVl+711z6eXFzMLIX81Gg7bk 55UkRwpxrVIe8meOA/H0JnneKn1FWb4U4ojdHJY7btbx/vVDoQu75mdz5Lp6+dPVIvCKUe +mrHnQ/QDbRiwFOAtO2Io9xryPK0NjnuaBK4QDCkIH7TVLxMZ17LB5IyLFNuUfQ1y0eb1m /PoiN12PM0fIhalmCrLuAA4OR6uPLt/iFov4A7CE7kiLTOsBRTgH6Q+D8en8JQ== 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=864d4fdd1804d2d4f46619f781e397b9ccdf1639 commit 864d4fdd1804d2d4f46619f781e397b9ccdf1639 Author: Jason W. Bacon AuthorDate: 2021-12-05 20:50:42 +0000 Commit: Jason W. Bacon CommitDate: 2021-12-05 20:50:42 +0000 biology/libgff: GFF/GTF parsing library based on GCLib This is an attempt to perform a simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase. There are not many (any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, and the goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn. Note: This library draws directly from the code in GFFRead and GCLib, and exists primarily to remove functionality (and hence code) that is unnecessary for our downstream purposes. In the future, it may be appropriate to just replace this library wholesale with GCLib. --- biology/Makefile | 1 + biology/libgff/Makefile | 16 ++++++++++++++++ biology/libgff/distinfo | 3 +++ biology/libgff/pkg-descr | 11 +++++++++++ biology/libgff/pkg-plist | 14 ++++++++++++++ 5 files changed, 45 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 02ba7b46b286..4e16a737f636 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -78,6 +78,7 @@ SUBDIR += kallisto SUBDIR += lamarc SUBDIR += libbigwig + SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml diff --git a/biology/libgff/Makefile b/biology/libgff/Makefile new file mode 100644 index 000000000000..6a16d0cd4557 --- /dev/null +++ b/biology/libgff/Makefile @@ -0,0 +1,16 @@ +PORTNAME= libgff +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= GFF/GTF parsing library based on GCLib + +LICENSE= BSL +LICENSE_FILE= ${WRKSRC}/BoostLicense.txt + +USES= cmake +USE_GITHUB= yes +GH_ACCOUNT= COMBINE-lab + +.include diff --git a/biology/libgff/distinfo b/biology/libgff/distinfo new file mode 100644 index 000000000000..9bb01692e5c1 --- /dev/null +++ b/biology/libgff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1631451501 +SHA256 (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c +SIZE (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 102152 diff --git a/biology/libgff/pkg-descr b/biology/libgff/pkg-descr new file mode 100644 index 000000000000..762881bedb74 --- /dev/null +++ b/biology/libgff/pkg-descr @@ -0,0 +1,11 @@ +This is an attempt to perform a simple "libraryfication" of the GFF/GTF +parsing code that is used in GFFRead codebase. There are not many +(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, +and the goal of this library is to provide this functionality without +the necessity of drawing in a heavy-weight dependency like SeqAn. Note: +This library draws directly from the code in GFFRead and GCLib, and +exists primarily to remove functionality (and hence code) that is +unnecessary for our downstream purposes. In the future, it may be +appropriate to just replace this library wholesale with GCLib. + +WWW: https://github.com/COMBINE-lab/libgff diff --git a/biology/libgff/pkg-plist b/biology/libgff/pkg-plist new file mode 100644 index 000000000000..474ea892d185 --- /dev/null +++ b/biology/libgff/pkg-plist @@ -0,0 +1,14 @@ +include/GArgs.h +include/GBase.h +include/GFaSeqGet.h +include/GFastaIndex.h +include/GHash.hh +include/GList.hh +include/GStr.h +include/GVec.hh +include/codons.h +include/gdna.h +include/gff.h +lib/libgff.a +lib/libgff/cmake/libgffConfig.cmake +lib/libgff/cmake/libgffConfigVersion.cmake