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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.
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@ -179,6 +179,7 @@
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SUBDIR += py-libsedml
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SUBDIR += py-loompy
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SUBDIR += py-macs2
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SUBDIR += py-macs3
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SUBDIR += py-mrcfile
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SUBDIR += py-multiqc
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SUBDIR += py-ont-fast5-api
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49
biology/py-macs3/Makefile
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49
biology/py-macs3/Makefile
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PORTNAME= MACS3
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DISTVERSIONPREFIX= v
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DISTVERSION= 3.0.0
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CATEGORIES= biology python
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Peak caller aimed at transcription factor binding sites
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WWW= https://github.com/taoliu/MACS
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE
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BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \
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${PYNUMPY} \
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simde>0:devel/simde \
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${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
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RUN_DEPENDS= ${PYNUMPY} \
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${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR}
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TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \
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bash:shells/bash
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USES= localbase perl5 python shebangfix
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USE_GITHUB= yes
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USE_PERL5= test
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USE_PYTHON= autoplist concurrent cython pep517
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GH_ACCOUNT= macs3-project
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GH_PROJECT= MACS
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SHEBANG_FILES= test/cmdlinetest* test/prockreport test/*.py test/pyprofile*
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.include <bsd.port.options.mk>
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.if ${OPSYS} == FreeBSD && ${OSVERSION} < 1302509
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IGNORE= does not run properly on FreeBSD 13.2 and earlier due to use of dynamically loaded libc by py-threadpoolctl. Please upgrade to a newer FreeBSD or use py-macs2 instead. See PR 276231
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.endif
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post-stage:
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${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS3/*/*.so
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# FIXME: Some tests fail due to a py-threadpoolctl issue
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# https://github.com/joblib/threadpoolctl/pull/148
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do-test: deinstall install
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@${RM} -rf ${WRKSRC}/temp
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@cd ${WRKSRC}/test && ./cmdlinetest tag
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.include <bsd.port.mk>
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biology/py-macs3/distinfo
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3
biology/py-macs3/distinfo
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TIMESTAMP = 1703890666
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SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d
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SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439
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biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
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biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c
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--- MACS3/fermi-lite/ksw.c.orig 2023-11-15 16:09:23 UTC
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+++ MACS3/fermi-lite/ksw.c
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@@ -28,7 +28,7 @@
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/* I modified this according to https://github.com/lh3/bwa/pull/283/*/
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#ifdef USE_SIMDE
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-#include "lib/x86/sse2.h"
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+#include <simde/x86/sse2.h>
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#else
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#include <emmintrin.h>
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#endif
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biology/py-macs3/files/patch-pyproject.toml
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biology/py-macs3/files/patch-pyproject.toml
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--- pyproject.toml.orig 2024-01-06 15:00:01 UTC
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+++ pyproject.toml
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@@ -1,2 +1,2 @@
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[build-system]
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-requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3']
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+requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3']
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biology/py-macs3/files/patch-requirements.txt
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biology/py-macs3/files/patch-requirements.txt
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--- requirements.txt.orig 2024-01-06 14:55:53 UTC
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+++ requirements.txt
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@@ -1,4 +1,4 @@
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-Cython~=3.0
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+Cython>=0
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numpy>=1.19
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hmmlearn>=0.3
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cykhash>=2.0,<3.0
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biology/py-macs3/files/patch-setup.py
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biology/py-macs3/files/patch-setup.py
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--- setup.py.orig 2023-11-15 16:09:23 UTC
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+++ setup.py
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@@ -40,7 +40,7 @@ classifiers =[\
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install_requires = [ "numpy>=1.19",
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"hmmlearn>=0.3",
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"cykhash>=2.0,<3.0",
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- "Cython~=3.0" ]
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+ "Cython>=0" ]
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tests_requires = [ 'pytest' ]
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@@ -70,7 +70,7 @@ def main():
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if not clang:
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try:
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- gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True)
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+ gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True)
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if gcc_version_check.find("clang") != -1:
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clang = True
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else:
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biology/py-macs3/pkg-descr
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6
biology/py-macs3/pkg-descr
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MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
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transcription factor (TF) binding sites. Such sites are generated
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by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
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(Assay for Transposase Accessible Chromatin Sequencing). MACS
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identifies "peaks" in the genome sequence, which are areas enriched
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in bound TFs or accessible chromatin.
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