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CVS commit: pkgsrc/biology/py-macs2
Module Name: pkgsrc
Committed By: bacon
Date: Sun Jan 22 23:30:11 UTC 2023
Added Files:
pkgsrc/biology/py-macs2: DESCR Makefile PLIST distinfo
pkgsrc/biology/py-macs2/patches: patch-setup.py
Log Message:
biology/py-macs2: Identify transcription factor binding sites
MACS is a tool for chromatin immunoprecipitation (ChIP) sequence
analysis. MACS empirically models the length of the sequenced ChIP
fragments, which tend to be shorter than sonication or library
construction size estimates, and uses it to improve the spatial
resolution of predicted binding sites.
To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/py-macs2/DESCR \
pkgsrc/biology/py-macs2/Makefile pkgsrc/biology/py-macs2/PLIST \
pkgsrc/biology/py-macs2/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/py-macs2/patches/patch-setup.py
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-macs2/DESCR
diff -u /dev/null pkgsrc/biology/py-macs2/DESCR:1.1
--- /dev/null Sun Jan 22 23:30:11 2023
+++ pkgsrc/biology/py-macs2/DESCR Sun Jan 22 23:30:11 2023
@@ -0,0 +1,5 @@
+MACS is a tool for chromatin immunoprecipitation (ChIP) sequence
+analysis. MACS empirically models the length of the sequenced ChIP
+fragments, which tend to be shorter than sonication or library
+construction size estimates, and uses it to improve the spatial
+resolution of predicted binding sites.
Index: pkgsrc/biology/py-macs2/Makefile
diff -u /dev/null pkgsrc/biology/py-macs2/Makefile:1.1
--- /dev/null Sun Jan 22 23:30:11 2023
+++ pkgsrc/biology/py-macs2/Makefile Sun Jan 22 23:30:11 2023
@@ -0,0 +1,29 @@
+# $NetBSD: Makefile,v 1.1 2023/01/22 23:30:11 bacon Exp $
+
+DISTNAME= MACS2-${PKGVERSION_NOREV}
+PKGNAME= ${PYPKGPREFIX}-macs2-2.2.7.1
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=taoliu/}
+GITHUB_PROJECT= MACS
+GITHUB_TAG= v${PKGVERSION_NOREV}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://github.com/macs3-project/MACS
+COMMENT= Algorithm for identifying transcription factor binding sites
+LICENSE= modified-bsd
+
+TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
+
+CYTHONIZE= ${PREFIX}/bin/cythonize-${PYVERSSUFFIX}
+
+# Distributed .c files do not support python > 3.9
+post-extract:
+ ${MV} ${WRKSRC}/MACS2/cPosValCalculation.c ${WRKSRC}
+ ${RM} ${WRKSRC}/MACS2/*.c ${WRKSRC}/MACS2/*/*.c
+ cd ${WRKSRC} && ${CYTHONIZE} ${WRKSRC}/MACS2/*.pyx
+ cd ${WRKSRC} && ${CYTHONIZE} ${WRKSRC}/MACS2/*/*.pyx
+ ${MV} ${WRKSRC}/cPosValCalculation.c ${WRKSRC}/MACS2
+
+.include "../../lang/python/egg.mk"
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/py-macs2/PLIST
diff -u /dev/null pkgsrc/biology/py-macs2/PLIST:1.1
--- /dev/null Sun Jan 22 23:30:11 2023
+++ pkgsrc/biology/py-macs2/PLIST Sun Jan 22 23:30:11 2023
@@ -0,0 +1,76 @@
+@comment $NetBSD: PLIST,v 1.1 2023/01/22 23:30:11 bacon Exp $
+bin/macs2
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/MACS2/Constants.py
+${PYSITELIB}/MACS2/Constants.pyc
+${PYSITELIB}/MACS2/Constants.pyo
+${PYSITELIB}/MACS2/IO/BedGraph.so
+${PYSITELIB}/MACS2/IO/BedGraphIO.so
+${PYSITELIB}/MACS2/IO/CallPeakUnit.so
+${PYSITELIB}/MACS2/IO/FixWidthTrack.so
+${PYSITELIB}/MACS2/IO/PairedEndTrack.so
+${PYSITELIB}/MACS2/IO/Parser.so
+${PYSITELIB}/MACS2/IO/PeakIO.so
+${PYSITELIB}/MACS2/IO/ScoreTrack.so
+${PYSITELIB}/MACS2/IO/__init__.py
+${PYSITELIB}/MACS2/IO/__init__.pyc
+${PYSITELIB}/MACS2/IO/__init__.pyo
+${PYSITELIB}/MACS2/OptValidator.py
+${PYSITELIB}/MACS2/OptValidator.pyc
+${PYSITELIB}/MACS2/OptValidator.pyo
+${PYSITELIB}/MACS2/OutputWriter.py
+${PYSITELIB}/MACS2/OutputWriter.pyc
+${PYSITELIB}/MACS2/OutputWriter.pyo
+${PYSITELIB}/MACS2/PeakDetect.so
+${PYSITELIB}/MACS2/PeakModel.so
+${PYSITELIB}/MACS2/Pileup.so
+${PYSITELIB}/MACS2/Prob.so
+${PYSITELIB}/MACS2/Signal.so
+${PYSITELIB}/MACS2/__init__.py
+${PYSITELIB}/MACS2/__init__.pyc
+${PYSITELIB}/MACS2/__init__.pyo
+${PYSITELIB}/MACS2/bdgbroadcall_cmd.py
+${PYSITELIB}/MACS2/bdgbroadcall_cmd.pyc
+${PYSITELIB}/MACS2/bdgbroadcall_cmd.pyo
+${PYSITELIB}/MACS2/bdgcmp_cmd.py
+${PYSITELIB}/MACS2/bdgcmp_cmd.pyc
+${PYSITELIB}/MACS2/bdgcmp_cmd.pyo
+${PYSITELIB}/MACS2/bdgdiff_cmd.py
+${PYSITELIB}/MACS2/bdgdiff_cmd.pyc
+${PYSITELIB}/MACS2/bdgdiff_cmd.pyo
+${PYSITELIB}/MACS2/bdgopt_cmd.py
+${PYSITELIB}/MACS2/bdgopt_cmd.pyc
+${PYSITELIB}/MACS2/bdgopt_cmd.pyo
+${PYSITELIB}/MACS2/bdgpeakcall_cmd.py
+${PYSITELIB}/MACS2/bdgpeakcall_cmd.pyc
+${PYSITELIB}/MACS2/bdgpeakcall_cmd.pyo
+${PYSITELIB}/MACS2/cPosValCalculation.pxd
+${PYSITELIB}/MACS2/callpeak_cmd.py
+${PYSITELIB}/MACS2/callpeak_cmd.pyc
+${PYSITELIB}/MACS2/callpeak_cmd.pyo
+${PYSITELIB}/MACS2/cmbreps_cmd.py
+${PYSITELIB}/MACS2/cmbreps_cmd.pyc
+${PYSITELIB}/MACS2/cmbreps_cmd.pyo
+${PYSITELIB}/MACS2/diffpeak_cmd.py
+${PYSITELIB}/MACS2/diffpeak_cmd.pyc
+${PYSITELIB}/MACS2/diffpeak_cmd.pyo
+${PYSITELIB}/MACS2/filterdup_cmd.py
+${PYSITELIB}/MACS2/filterdup_cmd.pyc
+${PYSITELIB}/MACS2/filterdup_cmd.pyo
+${PYSITELIB}/MACS2/khash.pxd
+${PYSITELIB}/MACS2/pileup_cmd.py
+${PYSITELIB}/MACS2/pileup_cmd.pyc
+${PYSITELIB}/MACS2/pileup_cmd.pyo
+${PYSITELIB}/MACS2/predictd_cmd.py
+${PYSITELIB}/MACS2/predictd_cmd.pyc
+${PYSITELIB}/MACS2/predictd_cmd.pyo
+${PYSITELIB}/MACS2/randsample_cmd.py
+${PYSITELIB}/MACS2/randsample_cmd.pyc
+${PYSITELIB}/MACS2/randsample_cmd.pyo
+${PYSITELIB}/MACS2/refinepeak_cmd.py
+${PYSITELIB}/MACS2/refinepeak_cmd.pyc
+${PYSITELIB}/MACS2/refinepeak_cmd.pyo
Index: pkgsrc/biology/py-macs2/distinfo
diff -u /dev/null pkgsrc/biology/py-macs2/distinfo:1.1
--- /dev/null Sun Jan 22 23:30:11 2023
+++ pkgsrc/biology/py-macs2/distinfo Sun Jan 22 23:30:11 2023
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2023/01/22 23:30:11 bacon Exp $
+
+BLAKE2s (MACS2-2.2.7.1.tar.gz) = 9018fcf83634355b625d8cbf6f67071c78d469bb35732318115470b7b7d30f8a
+SHA512 (MACS2-2.2.7.1.tar.gz) = 2591ff3258124b1d577b0f417838e13ca6151b011590dbb769fd500d7ee5c7969349a7e40d11c3d8cbe75555786f3b76d3950586d7ed144e6e7679018c32d5c5
+Size (MACS2-2.2.7.1.tar.gz) = 134872405 bytes
+SHA1 (patch-setup.py) = 9b17fd669b1d67aeb1e7ab8d8fc2b93624755f47
Index: pkgsrc/biology/py-macs2/patches/patch-setup.py
diff -u /dev/null pkgsrc/biology/py-macs2/patches/patch-setup.py:1.1
--- /dev/null Sun Jan 22 23:30:11 2023
+++ pkgsrc/biology/py-macs2/patches/patch-setup.py Sun Jan 22 23:30:11 2023
@@ -0,0 +1,35 @@
+$NetBSD: patch-setup.py,v 1.1 2023/01/22 23:30:11 bacon Exp $
+
+# Remove lexical version check and pip requirement
+
+--- setup.py.orig 2020-04-12 00:00:15.000000000 +0000
++++ setup.py
+@@ -20,28 +20,8 @@ numpy_requires = '>=1.17'
+ install_requires = [f"numpy>={numpy_requires}",]
+
+ def main():
+- if float(sys.version[:3])<3.6:
+- sys.stderr.write("CRITICAL: Python version must >= 3.6!\n")
+- sys.exit(1)
+-
+ cwd = os.path.abspath(os.path.dirname(__file__))
+
+- # install required numpy
+- p = subprocess.call([sys.executable, "-m", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)
+- if p != 0:
+- # Could be due to a too old pip version and build isolation, check that
+- try:
+- # Note, pip may not be installed or not have been used
+- import pip
+- if LooseVersion(pip.__version__) < LooseVersion('18.0.0'):
+- raise RuntimeError("Installing requirements failed. Possibly due "
+- "to `pip` being too old, found version {}, "
+- "needed is >= 18.0.0.".format(pip.__version__))
+- else:
+- raise RuntimeError("Installing requirements failed!")
+- except ImportError:
+- raise RuntimeError("Installing requirement failed! `pip` has to be installed!")
+-
+ from numpy import get_include as numpy_get_include
+ numpy_include_dir = [numpy_get_include()]
+
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