pyteomics Python modules for proteomics data analysis

2.4.0_1 science =0 2.4.0_1Version of this port present on the latest quarterly branch.

Maintainer: makc@FreeBSD.org

Port Added: 2013-03-28 13:05:57

Last Update: 2015-11-02 09:24:50

SVN Revision: 400643

Also Listed In: python

License: not specified in port

Description:

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis, such as: * calculation of basic physico-chemical properties of polypeptides: . mass and isotopic distribution . charge and pI . chromatographic retention time * access to common proteomics data: . MS or LC-MS data . FASTA databases . search engines output * easy manipulation of sequences of modified peptides and proteins WWW: https://pypi.python.org/pypi/pyteomics

SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:

• ${PYTHON_PKGNAMEPREFIX}pyteomics>0:science/pyteomics

No installation instructions: this port has been deleted.

The package name of this deleted port was: py27-pyteomics

PKGNAME: py27-pyteomics

Flavors: there is no flavor information for this port.

distinfo:

There is no distinfo for this port.

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

1. py27-setuptools27>0 : devel/py-setuptools27
2. python2.7 : lang/python27

Runtime dependencies:

1. py27-lxml>=0 : devel/py-lxml
2. py27-matplotlib>=0 : math/py-matplotlib
3. numeric.py : math/py-numpy
4. py27-setuptools27>0 : devel/py-setuptools27
5. python2.7 : lang/python27

There are no ports dependent upon this port

Configuration Options

No options to configure

USES:

python

Master Sites:

1. http://distcache.FreeBSD.org/ports-distfiles/
2. http://pypi.crate.io/packages/source/p/pyteomics/
3. http://pypi.python.jp/pyteomics/
4. http://pypi.python.org/packages/source/p/pyteomics/

• port moved to science/py-pyteomics on 2015-11-02
  REASON: Renamed to comply with Python ports policy
  

Rename my ports to comply with Python ports policy

Requested by:	koobs

- Convert ports of science/ and security to new USES=python

Approved by:	portmgr (implicit)

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

science/pyteomics:
- update to 2.4.0

science/pyteomics:
- update to 2.3.0

Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)

Update to 2.2.1

- Update to 2.2.0
- Use autoplist

Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui

- Support staging
- Use new LIB_DEPENDS syntax
- Use options helpers
- Convert to USES
- Minor changes/fixes

Add NO_STAGE all over the place in preparation for the staging support (cat:
science)

- Update to 2.1.5 and [1]:
- Allow to build with python3
- Simplify MASTER_SITES
- Don't remove python shared directories

Prompted by:	rm [1]

Add new port science/pyteomics:

Pyteomics is a collection of lightweight and handy tools for Python
that help to handle various sorts of proteomics data.  Pyteomics
provides a growing set of modules to facilitate the most common
tasks in proteomics data analysis, such as:
 * calculation of basic physico-chemical properties of polypeptides:
   . mass and isotopic distribution
   . charge and pI
   . chromatographic retention time
 * access to common proteomics data:
   . MS or LC-MS data
   . FASTA databases
   . search engines output
 * easy manipulation of sequences of modified peptides and proteins

WWW: https://pypi.python.org/pypi/pyteomics

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Last updated:
2020-07-11 12:42:41