BSD Portsbiology/py-deeptools 3.5.6 FreeBSD
User-friendly tools for exploring deep-sequencing data
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- BSD3CLAUSE
- Categories
- biology, python
- Package size
- 376.9 KiB, 2273.3 KiB installed
Description
deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/py-deeptools | 3.5.6 |
| DragonFly | biology/py-deeptools | 3.5.2_1 |
| HardenedBSD | biology/py-deeptools | 3.5.6 |
| GhostBSD | biology/py-deeptools | 3.5.6 |
Install
Binary package:
pkg install py312-deepToolsFrom the ports tree:
cd /usr/ports/biology/py-deeptools/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= py312-deepTools>0:biology/py-deeptoolsPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 3.5.6 | 3.5.6 | - | - | 3.5.6 |
| FreeBSD:14:quarterly | 3.5.6 | 3.5.6 | n/a | - | 3.5.6 |
| FreeBSD:15:latest | 3.5.6 | 3.5.6 | n/a | - | 3.5.2_1 |
| FreeBSD:15:quarterly | 3.5.6 | 3.5.6 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.5.6 | 3.5.6 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 2
${PYTHON_PKGNAMEPREFIX}setuptools>0: devel/py-setuptools${PYTHON_PKGNAMEPREFIX}wheel>0: devel/py-wheel
Runtime 8
${PYTHON_PKGNAMEPREFIX}scipy>=0.17.0: science/py-scipy${PYTHON_PKGNAMEPREFIX}matplotlib>=3.5.0: math/py-matplotlib${PYTHON_PKGNAMEPREFIX}pysam>=0.14.0: biology/py-pysam${PYTHON_PKGNAMEPREFIX}py2bit>=0.2.0: biology/py-py2bit${PYTHON_PKGNAMEPREFIX}numpydoc>=0.5: textproc/py-numpydoc${PYTHON_PKGNAMEPREFIX}pyBigWig>=0.2.1: biology/py-pybigwig${PYTHON_PKGNAMEPREFIX}plotly>=4.9: graphics/py-plotly${PYTHON_PKGNAMEPREFIX}deeptoolsintervals>=0.1.8: biology/py-deeptoolsintervals
The full lists below include those, and their dependencies in turn.
Build dependencies 16
Run dependencies 128
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/py-brotli
- archivers/py-zopfli
- archivers/zopfli
- archivers/zstd
- biology/bcftools
- biology/htslib
- biology/py-deeptoolsintervals
- biology/py-py2bit
- biology/py-pybigwig
- biology/py-pysam
- biology/samtools
- converters/fribidi
- converters/libiconv
- devel/binutils
- devel/gettext-runtime
- devel/glib20
- devel/libffi
- devel/libinotify
- devel/libunistring
- devel/pcre2
- devel/py-Jinja2
- devel/py-babel
- devel/py-cycler
- devel/py-lxml
- devel/py-olefile
- devel/py-packaging
- devel/py-pyparsing
- devel/py-python-dateutil
- devel/py-six
- devel/py-tabulate
- devel/py-typing-extensions
- devel/py-unicodedata2
- devel/py-wcwidth
- devel/readline
- dns/libidn2
- dns/libpsl
- dns/py-idna
- ftp/curl
- graphics/gdk-pixbuf2
- graphics/giflib
- graphics/graphite2
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/libavif
- graphics/libimagequant
- graphics/libyuv
- graphics/openjpeg
- graphics/png
- graphics/py-imagesize
- graphics/py-pillow
- graphics/py-plotly
- graphics/tiff
- graphics/webp
- lang/cython
- lang/gcc14
- lang/perl5.42
- lang/python312
- lang/python315
- lang/tcl86
- math/gmp
- math/gsl
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-contourpy
- math/py-kiwisolver
- math/py-matplotlib
- math/py-narwhals
- math/py-numpy
- math/qhull
- misc/shared-mime-info
- multimedia/aom
- multimedia/dav1d
- multimedia/vmaf
- net/py-pysocks
- net/py-urllib3
- print/freetype2
- print/harfbuzz
- print/indexinfo
- print/libraqm
- print/py-fonttools
- science/py-scipy
- security/ca_root_nss
- security/libgcrypt
- security/libgpg-error
- security/libssh2
- security/py-certifi
- shells/bash
- textproc/expat2
- textproc/libxml2
- textproc/libxslt
- textproc/py-alabaster
- textproc/py-charset-normalizer
- textproc/py-docutils
The first 100 are listed.
Required by 1
Configuration
No options to configure.
- USES
- python
- Service scripts
- none
Message after installing
===> NOTICE: The py312-deepTools port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| deeptools-3.5.6.tar.gz | 199316 | 2daf06abc8cf2df42f7e0ecacb3784ee95de1db4dd887f69f22a29f27e202369 |
Master sites 1
- PYPI