From nobody Fri Nov 22 20:36:03 2024 X-Original-To: dev-commits-ports-all@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 4Xw6Lr1C0Tz5dLjW; Fri, 22 Nov 2024 20:36:04 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Xw6Lr01hdz4Wd7; Fri, 22 Nov 2024 20:36:04 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1732307764; 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=YUUHp+I/Rn31AbOVAwtFDTc641AYDSEcgEjVm2qRwxY=; b=UeitFvBz++zI9ICcsWmS4lemWEfciUFpSiOU6HZ5Ztf+86o7z5W0R20lpKBs28S2dmTkjD g5Faa50g1aknoQNSd80Mv7EhC80JlKprkfJfEKC1tZsiNYl+YiGnnjNf3dB5gaVKReHasi lx/ICq0vGGIS/tnmFL4K0Uo1cHIUG8WUWlsBZiYgKR3h1sRekDg/fo1Q0Jbr5YelT+nFVz dXF/c54vKwkAjEeDn4fA34lquX04ZX+UhJFh4Fs0TaOsky1m/j3x2JPV81MfJSjPxjntEZ T12sYxHwrj2zMCJfklJ/zw/CWUk+ynp9S4c2uYwXe9ukaKQYuXqaPeMHKce9pQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1732307764; 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=YUUHp+I/Rn31AbOVAwtFDTc641AYDSEcgEjVm2qRwxY=; b=OvrDYsFASsrbOZmhV8KuD1tlN+tQqqbvltYPyAIYSeEposn+n168nCfACes9wr0yVZMSEi jqyG2oiiMCh2ZDBoamN6R2iWaf0Vilp19ThCHYZy/zXe6UqmtKi8Ja/h/devxL7x+hB5mF xK1v0jIdNl1ARjzNVznwKspEkVz4Any3c7ZvqUQ/1H/X6FTxF/PTnW6XzUKX8JfeH+mqOA VYhK+HtBMNP/So0S9HC3LDyhRpTpmkXGlxlSyBiMen9LArWddcqO30BzIrFqa09pmbqq2o HccK1qJ2unhiJEZGrluiP4wpQCeXL2FEoUetlllPwDQsqpED7sgeKK4WurCd4g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1732307764; a=rsa-sha256; cv=none; b=IXwA18hq1xtGj0plzdH9E+qbYm1ZMoQiweSQ9MTCzn33habZAKRB6ZYECnOIBiWUo8Kf3P lTaTBCPb49mRIoTtVqcKpO6M1qIkWVCsi9N/ThErVTKM15o3oT2uf347gfp5+n51g0RQnG suWiZueBe4J0SZawNAdfakkRC+nlxbxD99haTxa5ROAnin/Xt8PxEHnQAdkB/tC++uUIGg MGLHbIonk5rNSqbAPbt02LHEPLZyF+xdUxNhbdxZtf3T/qG3qLf29e78XewEV6nwJ/5HhE OfzGigfH4TzBCWiTmWMGqdKihNzRMvxFCaUtabRmAZts+D4jhKhA5OWAxHuEoA== 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 4Xw6Lq6kXmzflg; Fri, 22 Nov 2024 20:36:03 +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 4AMKa3Vh094921; Fri, 22 Nov 2024 20:36:03 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4AMKa304094916; Fri, 22 Nov 2024 20:36:03 GMT (envelope-from git) Date: Fri, 22 Nov 2024 20:36:03 GMT Message-Id: <202411222036.4AMKa304094916@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: af7a74db0001 - main - biology/preseq: Predict yield of distinct reads from a genomic library List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@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: af7a74db0001a2996b12a6e45c3ac235b92647b7 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=af7a74db0001a2996b12a6e45c3ac235b92647b7 commit af7a74db0001a2996b12a6e45c3ac235b92647b7 Author: Jason W. Bacon AuthorDate: 2024-11-22 20:35:51 +0000 Commit: Jason W. Bacon CommitDate: 2024-11-22 20:35:51 +0000 biology/preseq: Predict yield of distinct reads from a genomic library The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples. --- biology/Makefile | 1 + biology/preseq/Makefile | 21 +++++++++++++++++++++ biology/preseq/distinfo | 3 +++ biology/preseq/pkg-descr | 5 +++++ biology/preseq/pkg-plist | 17 +++++++++++++++++ 5 files changed, 47 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 3f12e044804a..35727e12139c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -156,6 +156,7 @@ SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler + SUBDIR += preseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig diff --git a/biology/preseq/Makefile b/biology/preseq/Makefile new file mode 100644 index 000000000000..f25bd80cbe9d --- /dev/null +++ b/biology/preseq/Makefile @@ -0,0 +1,21 @@ +PORTNAME= preseq +DISTVERSION= 3.2.0 +CATEGORIES= biology +# Github-generated distfiles are incomplete +MASTER_SITES= https://github.com/smithlabcode/preseq/releases/download/v${DISTVERSION}/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Predict yield of distinct reads from a genomic library +WWW= https://github.com/smithlabcode/preseq + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libhts.so:biology/htslib + +USES= localbase + +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --enable-hts + +.include diff --git a/biology/preseq/distinfo b/biology/preseq/distinfo new file mode 100644 index 000000000000..6a9390f4dbc5 --- /dev/null +++ b/biology/preseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1732301093 +SHA256 (preseq-3.2.0.tar.gz) = 95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9 +SIZE (preseq-3.2.0.tar.gz) = 6488708 diff --git a/biology/preseq/pkg-descr b/biology/preseq/pkg-descr new file mode 100644 index 000000000000..3e9357056178 --- /dev/null +++ b/biology/preseq/pkg-descr @@ -0,0 +1,5 @@ +The preseq package is aimed at predicting the yield of distinct reads +from a genomic library from an initial sequencing experiment. The +estimates can then be used to examine the utility of further +sequencing, optimize the sequencing depth, or to screen multiple +libraries to avoid low complexity samples. diff --git a/biology/preseq/pkg-plist b/biology/preseq/pkg-plist new file mode 100644 index 000000000000..b876eadc3daf --- /dev/null +++ b/biology/preseq/pkg-plist @@ -0,0 +1,17 @@ +bin/preseq +bin/to-mr +include/GenomicRegion.hpp +include/MappedRead.hpp +include/OptionParser.hpp +include/QualityScore.hpp +include/bisulfite_utils.hpp +include/chromosome_utils.hpp +include/cigar_utils.hpp +include/dna_four_bit.hpp +include/htslib_wrapper_deprecated.hpp +include/sam_record.hpp +include/sim_utils.hpp +include/smithlab_os.hpp +include/smithlab_utils.hpp +include/zlib_wrapper.hpp +lib/libsmithlab_cpp.a