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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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Jason W. Bacon
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Jason W. Bacon
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Jan 10, 2024
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PORTNAME= MACS3 | ||
DISTVERSIONPREFIX= v | ||
DISTVERSION= 3.0.0 | ||
CATEGORIES= biology python | ||
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} | ||
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MAINTAINER= jwb@FreeBSD.org | ||
COMMENT= Peak caller aimed at transcription factor binding sites | ||
WWW= https://github.com/taoliu/MACS | ||
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LICENSE= BSD3CLAUSE | ||
LICENSE_FILE= ${WRKSRC}/LICENSE | ||
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BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ | ||
${PYNUMPY} \ | ||
simde>0:devel/simde \ | ||
${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ | ||
${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} | ||
RUN_DEPENDS= ${PYNUMPY} \ | ||
${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ | ||
${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} | ||
TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ | ||
bash:shells/bash | ||
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USES= localbase perl5 python shebangfix | ||
USE_GITHUB= yes | ||
USE_PERL5= test | ||
USE_PYTHON= autoplist concurrent cython pep517 | ||
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GH_ACCOUNT= macs3-project | ||
GH_PROJECT= MACS | ||
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 | ||
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 | ||
.endif | ||
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post-stage: | ||
${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS3/*/*.so | ||
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# FIXME: Some tests fail due to a py-threadpoolctl issue | ||
# https://github.com/joblib/threadpoolctl/pull/148 | ||
do-test: deinstall install | ||
@${RM} -rf ${WRKSRC}/temp | ||
@cd ${WRKSRC}/test && ./cmdlinetest tag | ||
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.include <bsd.port.mk> |
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TIMESTAMP = 1703890666 | ||
SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d | ||
SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439 |
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--- MACS3/fermi-lite/ksw.c.orig 2023-11-15 16:09:23 UTC | ||
+++ MACS3/fermi-lite/ksw.c | ||
@@ -28,7 +28,7 @@ | ||
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/* 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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--- pyproject.toml.orig 2024-01-06 15:00:01 UTC | ||
+++ pyproject.toml | ||
@@ -1,2 +1,2 @@ | ||
[build-system] | ||
-requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3'] | ||
+requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3'] |
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--- requirements.txt.orig 2024-01-06 14:55:53 UTC | ||
+++ requirements.txt | ||
@@ -1,4 +1,4 @@ | ||
-Cython~=3.0 | ||
+Cython>=0 | ||
numpy>=1.19 | ||
hmmlearn>=0.3 | ||
cykhash>=2.0,<3.0 |
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--- setup.py.orig 2023-11-15 16:09:23 UTC | ||
+++ setup.py | ||
@@ -40,7 +40,7 @@ classifiers =[\ | ||
install_requires = [ "numpy>=1.19", | ||
"hmmlearn>=0.3", | ||
"cykhash>=2.0,<3.0", | ||
- "Cython~=3.0" ] | ||
+ "Cython>=0" ] | ||
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tests_requires = [ 'pytest' ] | ||
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@@ -70,7 +70,7 @@ def main(): | ||
if not clang: | ||
try: | ||
- gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True) | ||
+ gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True) | ||
if gcc_version_check.find("clang") != -1: | ||
clang = True | ||
else: |
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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. |