CVS commit: pkgsrc/biology/py-macs3

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/py-macs3
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Wed, 10 Jan 2024 15:17:34 +0000

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.

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@localhost
+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 <simde/x86/sse2.h>
+ #else
+ #include <emmintrin.h>
+ #endif

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