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.
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above. NOTE: This is a Python port. Instead of py312-MACS3 listed in the above command, you can pick from the names under the Packages section.
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
- Update USE_PYTHON=cython{,_run,_test}
- Convert all cython3 occurrence to USE_PYTHON=cython3*
- While I'm here, fix incorrect usage of combining cython3 in BUILD_DEPENDS and
USE_PYTHON=cython
It is added to simplify the future transition from Cython 0.29 to 3.
The minimal version is set to 3.0.12 because it is required by
devel/py-propcache.
The upper bound of version is set to 3.1 because it is limited by multiple
ports.
biology/py-macs3: Unbreak package build
pep57 -> distutils
Port passed poudriere before, but spontaneously broke due to
other changes
Reported by: pkg-fallout
all: drop support for FreeBSD 13.2 which reached EOL today
Thanks again to jbeich for noticing various things I overlooked.
Reviewed by: acm, ashish, eduardo, ehaupt, eugen, jbeich, martymac, mat,
nobukata, sunpoet, tagattie, yuri, arrowd, kde
Differential Revision: https://reviews.freebsd.org/D45141
*/*: Add ${PY_SETUPTOOLS} to BUILD_DEPENDS
Fix build when setuptools is removed from RUN_DEPENDS in
Mk/Uses/python.mk.
PR: 270510
Approved by: portmgr (blanket)
biology/py-macs3: Mark not for i386
SIMDE does not support _Float16
Nobody does bioinformatics on 32-bit processors anyway, as many
applications have huge memory requirements
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.
