Received: by mail.netbsd.org (Postfix, from userid 605) id 27B178501A; Wed, 10 Jan 2024 15:17:36 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 53B8285018 for ; Wed, 10 Jan 2024 15:17:35 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id pdGay1DUs396 for ; Wed, 10 Jan 2024 15:17:34 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 4259684CD7 for ; Wed, 10 Jan 2024 15:17:34 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 2DA8EFA42; Wed, 10 Jan 2024 15:17:34 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1704899854294490" MIME-Version: 1.0 Date: Wed, 10 Jan 2024 15:17:34 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/py-macs3 To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20240110151734.2DA8EFA42@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1704899854294490 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Wed Jan 10 15:17:34 UTC 2024 Added Files: pkgsrc/biology/py-macs3: DESCR Makefile PLIST distinfo pkgsrc/biology/py-macs3/patches: patch-MACS3_fermi-lite_ksw.c Log Message: biology/py-macs3: Peak caller for TF binding sites MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying transcription factor (TF) binding sites. Such sites are generated by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq (Assay for Transposase Accessible Chromatin Sequencing). MACS identifies "peaks" in the genome sequence, which are areas enriched in bound TFs or accessible chromatin. To generate a diff of this commit: cvs rdiff -u -r0 -r1.1 pkgsrc/biology/py-macs3/DESCR \ pkgsrc/biology/py-macs3/Makefile pkgsrc/biology/py-macs3/PLIST \ pkgsrc/biology/py-macs3/distinfo cvs rdiff -u -r0 -r1.1 \ pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1704899854294490 Content-Disposition: inline Content-Length: 8104 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Added files: Index: pkgsrc/biology/py-macs3/DESCR diff -u /dev/null pkgsrc/biology/py-macs3/DESCR:1.1 --- /dev/null Wed Jan 10 15:17:34 2024 +++ pkgsrc/biology/py-macs3/DESCR Wed Jan 10 15:17:33 2024 @@ -0,0 +1,6 @@ +MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying +transcription factor (TF) binding sites. Such sites are generated +by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq +(Assay for Transposase Accessible Chromatin Sequencing). MACS +identifies "peaks" in the genome sequence, which are areas enriched +in bound TFs or accessible chromatin. Index: pkgsrc/biology/py-macs3/Makefile diff -u /dev/null pkgsrc/biology/py-macs3/Makefile:1.1 --- /dev/null Wed Jan 10 15:17:34 2024 +++ pkgsrc/biology/py-macs3/Makefile Wed Jan 10 15:17:33 2024 @@ -0,0 +1,34 @@ +# $NetBSD: Makefile,v 1.1 2024/01/10 15:17:33 bacon Exp $ + +DISTNAME= macs-${PKGVERSION_NOREV} +PKGNAME= ${PYPKGPREFIX}-macs3-3.0.0 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=macs3-project/} +GITHUB_PROJECT= MACS +GITHUB_TAG= v${PKGVERSION_NOREV} + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= https://github.com/macs3-project/MACS +COMMENT= Peak caller aimed at transcription factor binding sites +LICENSE= modified-bsd + +TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=0:../../devel/py-setuptools +TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel>=0:../../devel/py-wheel +DEPENDS+= ${PYPKGPREFIX}-hmmlearn>=0.3:../../math/py-hmmlearn +# cykhash>=2.0,<3.0 +DEPENDS+= ${PYPKGPREFIX}-cykhash>=2.0:../../devel/py-cykhash +TEST_DEPENDS= ${PYPKGPREFIX}-test>=7.0:../../devel/py-test + +USE_TOOLS+= bash perl:test +REPLACE_BASH= test/cmdlinetest* test/prockreport test/*.py test/pyprofile* + +do-test: install + ${RM} -rf ${WRKSRC}/temp + (cd ${WRKSRC}/test && ./cmdlinetest tag) + +.include "../../lang/python/wheel.mk" +.include "../../math/py-numpy/buildlink3.mk" +.include "../../devel/py-cython/buildlink3.mk" +.include "../../devel/simde/buildlink3.mk" +.include "../../devel/zlib/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" Index: pkgsrc/biology/py-macs3/PLIST diff -u /dev/null pkgsrc/biology/py-macs3/PLIST:1.1 --- /dev/null Wed Jan 10 15:17:34 2024 +++ pkgsrc/biology/py-macs3/PLIST Wed Jan 10 15:17:33 2024 @@ -0,0 +1,104 @@ +@comment $NetBSD: PLIST,v 1.1 2024/01/10 15:17:33 bacon Exp $ +bin/macs3 +${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/LICENSE +${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/METADATA +${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/RECORD +${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/WHEEL +${PYSITELIB}/MACS3-${PKGVERSION}.dist-info/top_level.txt +${PYSITELIB}/MACS3/Commands/__init__.py +${PYSITELIB}/MACS3/Commands/__init__.pyc +${PYSITELIB}/MACS3/Commands/__init__.pyo +${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.py +${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyc +${PYSITELIB}/MACS3/Commands/bdgbroadcall_cmd.pyo +${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.py +${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.pyc +${PYSITELIB}/MACS3/Commands/bdgcmp_cmd.pyo +${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.py +${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.pyc +${PYSITELIB}/MACS3/Commands/bdgdiff_cmd.pyo +${PYSITELIB}/MACS3/Commands/bdgopt_cmd.py +${PYSITELIB}/MACS3/Commands/bdgopt_cmd.pyc +${PYSITELIB}/MACS3/Commands/bdgopt_cmd.pyo +${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.py +${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.pyc +${PYSITELIB}/MACS3/Commands/bdgpeakcall_cmd.pyo +${PYSITELIB}/MACS3/Commands/callpeak_cmd.py +${PYSITELIB}/MACS3/Commands/callpeak_cmd.pyc +${PYSITELIB}/MACS3/Commands/callpeak_cmd.pyo +${PYSITELIB}/MACS3/Commands/callvar_cmd.py +${PYSITELIB}/MACS3/Commands/callvar_cmd.pyc +${PYSITELIB}/MACS3/Commands/callvar_cmd.pyo +${PYSITELIB}/MACS3/Commands/cmbreps_cmd.py +${PYSITELIB}/MACS3/Commands/cmbreps_cmd.pyc +${PYSITELIB}/MACS3/Commands/cmbreps_cmd.pyo +${PYSITELIB}/MACS3/Commands/diffpeak_cmd.py +${PYSITELIB}/MACS3/Commands/diffpeak_cmd.pyc +${PYSITELIB}/MACS3/Commands/diffpeak_cmd.pyo +${PYSITELIB}/MACS3/Commands/filterdup_cmd.py +${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyc +${PYSITELIB}/MACS3/Commands/filterdup_cmd.pyo +${PYSITELIB}/MACS3/Commands/hmmratac_cmd.py +${PYSITELIB}/MACS3/Commands/hmmratac_cmd.pyc +${PYSITELIB}/MACS3/Commands/hmmratac_cmd.pyo +${PYSITELIB}/MACS3/Commands/pileup_cmd.py +${PYSITELIB}/MACS3/Commands/pileup_cmd.pyc +${PYSITELIB}/MACS3/Commands/pileup_cmd.pyo +${PYSITELIB}/MACS3/Commands/predictd_cmd.py +${PYSITELIB}/MACS3/Commands/predictd_cmd.pyc +${PYSITELIB}/MACS3/Commands/predictd_cmd.pyo +${PYSITELIB}/MACS3/Commands/randsample_cmd.py +${PYSITELIB}/MACS3/Commands/randsample_cmd.pyc +${PYSITELIB}/MACS3/Commands/randsample_cmd.pyo +${PYSITELIB}/MACS3/Commands/refinepeak_cmd.py +${PYSITELIB}/MACS3/Commands/refinepeak_cmd.pyc +${PYSITELIB}/MACS3/Commands/refinepeak_cmd.pyo +${PYSITELIB}/MACS3/IO/BAM.so +${PYSITELIB}/MACS3/IO/BedGraphIO.so +${PYSITELIB}/MACS3/IO/OutputWriter.py +${PYSITELIB}/MACS3/IO/OutputWriter.pyc +${PYSITELIB}/MACS3/IO/OutputWriter.pyo +${PYSITELIB}/MACS3/IO/Parser.so +${PYSITELIB}/MACS3/IO/PeakIO.so +${PYSITELIB}/MACS3/IO/__init__.py +${PYSITELIB}/MACS3/IO/__init__.pyc +${PYSITELIB}/MACS3/IO/__init__.pyo +${PYSITELIB}/MACS3/Signal/BedGraph.so +${PYSITELIB}/MACS3/Signal/CallPeakUnit.so +${PYSITELIB}/MACS3/Signal/FixWidthTrack.so +${PYSITELIB}/MACS3/Signal/HMMR_EM.so +${PYSITELIB}/MACS3/Signal/HMMR_HMM.so +${PYSITELIB}/MACS3/Signal/HMMR_Signal_Processing.so +${PYSITELIB}/MACS3/Signal/PairedEndTrack.so +${PYSITELIB}/MACS3/Signal/PeakDetect.so +${PYSITELIB}/MACS3/Signal/PeakModel.so +${PYSITELIB}/MACS3/Signal/PeakVariants.so +${PYSITELIB}/MACS3/Signal/Pileup.so +${PYSITELIB}/MACS3/Signal/PileupV2.so +${PYSITELIB}/MACS3/Signal/PosReadsInfo.so +${PYSITELIB}/MACS3/Signal/Prob.so +${PYSITELIB}/MACS3/Signal/RACollection.so +${PYSITELIB}/MACS3/Signal/ReadAlignment.so +${PYSITELIB}/MACS3/Signal/Region.so +${PYSITELIB}/MACS3/Signal/ScoreTrack.so +${PYSITELIB}/MACS3/Signal/SignalProcessing.so +${PYSITELIB}/MACS3/Signal/UnitigRACollection.so +${PYSITELIB}/MACS3/Signal/VariantStat.so +${PYSITELIB}/MACS3/Signal/__init__.py +${PYSITELIB}/MACS3/Signal/__init__.pyc +${PYSITELIB}/MACS3/Signal/__init__.pyo +${PYSITELIB}/MACS3/Utilities/Constants.py +${PYSITELIB}/MACS3/Utilities/Constants.pyc +${PYSITELIB}/MACS3/Utilities/Constants.pyo +${PYSITELIB}/MACS3/Utilities/Logger.py +${PYSITELIB}/MACS3/Utilities/Logger.pyc +${PYSITELIB}/MACS3/Utilities/Logger.pyo +${PYSITELIB}/MACS3/Utilities/OptValidator.py +${PYSITELIB}/MACS3/Utilities/OptValidator.pyc +${PYSITELIB}/MACS3/Utilities/OptValidator.pyo +${PYSITELIB}/MACS3/Utilities/__init__.py +${PYSITELIB}/MACS3/Utilities/__init__.pyc +${PYSITELIB}/MACS3/Utilities/__init__.pyo +${PYSITELIB}/MACS3/__init__.py +${PYSITELIB}/MACS3/__init__.pyc +${PYSITELIB}/MACS3/__init__.pyo Index: pkgsrc/biology/py-macs3/distinfo diff -u /dev/null pkgsrc/biology/py-macs3/distinfo:1.1 --- /dev/null Wed Jan 10 15:17:34 2024 +++ pkgsrc/biology/py-macs3/distinfo Wed Jan 10 15:17:33 2024 @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2024/01/10 15:17:33 bacon Exp $ + +BLAKE2s (macs-3.0.0.tar.gz) = 6a28a732c0cef04e57c27f1679f372b40a48dc1aba23d8daa0555c63e02aa1bd +SHA512 (macs-3.0.0.tar.gz) = 44daa10901cea110ae6d0a5749e9696fa64883151b11af6b13c8d4ae589bc3207048d0de4420308a922a96b5dd542b694897ceabaac32becc07aef0061ee2257 +Size (macs-3.0.0.tar.gz) = 197389439 bytes +SHA1 (patch-MACS3_fermi-lite_ksw.c) = 7df96d1d970a3e70c4611bd618d1aa539297dbcc Index: pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c diff -u /dev/null pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c:1.1 --- /dev/null Wed Jan 10 15:17:34 2024 +++ pkgsrc/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c Wed Jan 10 15:17:33 2024 @@ -0,0 +1,15 @@ +$NetBSD: patch-MACS3_fermi-lite_ksw.c,v 1.1 2024/01/10 15:17:33 bacon Exp $ + +# Use SIMDE sse2.h + +--- MACS3/fermi-lite/ksw.c.orig 2023-12-21 22:20:16.716124047 +0000 ++++ MACS3/fermi-lite/ksw.c +@@ -28,7 +28,7 @@ + + /* I modified this according to https://github.com/lh3/bwa/pull/283/*/ + #ifdef USE_SIMDE +-#include "lib/x86/sse2.h" ++#include + #else + #include + #endif --_----------=_1704899854294490--