| Port details |
- py-deeptools User-friendly tools for exploring deep-sequencing data
- 3.5.2 biology
 =2      3.5.2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-10-14 11:57:05
- Last Update: 2023-06-19 12:09:17
- Commit Hash: e24fe4f
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: BSD3CLAUSE
- WWW:
- https://github.com/deeptools/deepTools
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-deeptools/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-deeptools
- pkg install py39-deepTools
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 py39-deepTools listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-deepTools
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1687035894
SHA256 (deepTools-3.5.2.tar.gz) = 9367f9037b1822b7d69d5abaf47ca25bf0e5dc4cb8be85bd55b6f63c90781941
SIZE (deepTools-3.5.2.tar.gz) = 203152
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-scipy>=0.17.0 : science/py-scipy@py39
- py39-matplotlib>=3.3.0 : math/py-matplotlib@py39
- py39-pysam>=0.14.0 : biology/py-pysam@py39
- py39-py2bit>=0.3.0 : biology/py-py2bit@py39
- py39-numpydoc>=0.5 : textproc/py-numpydoc@py39
- py39-pyBigWig>=0.3.18 : biology/py-pybigwig@py39
- py39-plotly>=4.9 : graphics/py-plotly@py39
- py39-deeptoolsintervals>=0.1.8 : biology/py-deeptoolsintervals@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_py-deeptools
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 6
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
3.5.2
19 Jun 2023 12:09:17
 |
Jason W. Bacon (jwb) |
biology/py-deeptools: Update to 3.5.2
Numerous enhancements and bug fixes
Changes: https://github.com/deeptools/deepTools/releases |
3.5.1_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
3.5.1
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
3.5.1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
3.5.1
14 Oct 2021 11:51:12
|
Jason W. Bacon (jwb) |
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
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. |
Number of commits found: 6
|
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