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Things are slow!

Some of the pages ont the website are slow. I know diskio is way up. I don't know what it is but it's been going on for about three weeks. It might have been a change to the zpool recordsize on the PostgreSQL database dataset.

One way to know: copy the dataset to another dataset with the original recordsize and use that. I hope can get to that later this week.

I have not tackled the issue yet because I've been concentrating on the BSDCan and PGCon calls for papers.

Port details
py-pysam Python module for reading, manipulating and writing genomic data sets
0.15.3 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.15.2Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-05-06 06:30:42
Last Update: 2019-08-31 16:49:19
SVN Revision: 510398
Also Listed In: python
License: MIT
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • py36-pysam>0:biology/py-pysam
To install the port: cd /usr/ports/biology/py-pysam/ && make install clean
To add the package: pkg install py36-pysam
PKGNAME: py36-pysam
Package flavors (<flavor>: <package>)
  • py36: py36-pysam
  • py27: py27-pysam
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. cython-3.6 : lang/cython@py36
  3. py36-setuptools>0 : devel/py-setuptools@py36
  4. python3.6 : lang/python36
Runtime dependencies:
  1. cython-3.6 : lang/cython@py36
  2. py36-setuptools>0 : devel/py-setuptools@py36
  3. python3.6 : lang/python36
This port is required by:
for Run
  1. biology/checkm

Configuration Options

USES:

Master Sites:
  1. https://files.pythonhosted.org/packages/source/p/pysam/
  2. https://pypi.org/packages/source/p/pysam/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
31 Aug 2019 15:49:19
Original commit files touched by this commit  0.15.3
Revision:510398
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.2 -> 0.15.3

Reported by:	portscout
26 Jan 2019 04:15:54
Original commit files touched by this commit  0.15.2
Revision:491232
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.1 -> 0.15.2

Reported by:	portscout
17 Sep 2018 17:40:28
Original commit files touched by this commit  0.15.1
Revision:479938
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.0 -> 0.15.1

Reported by:	portscout
30 Jul 2018 19:47:50
Original commit files touched by this commit  0.15.0
Revision:475906
yuri search for other commits by this committer
biology/py-pysam: Update 0.14.1 -> 0.15.0

Port changes:
* Remove stripping: done by the project now
* Update WWW

Reported by:	portscout
25 Apr 2018 16:42:38
Original commit files touched by this commit  0.14.1
Revision:468282
amdmi3 search for other commits by this committer
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
they now redirect to anyway. All new urls checked to return 200,
I've fixed a couple of them in the process.

Approved by:	portmgr blanket, mat
21 Mar 2018 08:12:33
Original commit files touched by this commit  0.14.1
Revision:465157
yuri search for other commits by this committer
biology/py-pysam: Update to 0.14.1

Also silenced STRIP_CMD.

Reported by:	portscout
10 Feb 2018 23:01:38
Original commit files touched by this commit  0.14
Revision:461449
yuri search for other commits by this committer
biology/py-pysam: Update to 0.14

Changelog:
https://github.com/pysam-developers/pysam/releases/tag/v0.14

Reported by:	portscout
Approved by:	tcberner (mentor, implicit)
30 Nov 2017 15:50:34
Original commit files touched by this commit  0.13
Revision:455210  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
05 Nov 2017 19:12:29
Original commit files touched by this commit  0.13
Revision:453556
yuri search for other commits by this committer
biology/py-pysam: Update to 0.13

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D12967
26 Oct 2017 05:30:35
Original commit files touched by this commit  0.12.0.1
Revision:452904
tcberner search for other commits by this committer
Update biology/py-pysam to 0.12.0.1

PR:		223254
Submitted by:	Yuri Victorovich <yuri@rawbw.com> (maintainer)
10 Jun 2017 02:03:39
Original commit files touched by this commit  0.11.2.2
Revision:443056
wen search for other commits by this committer
- Update to 0.11.2.2

PR:		219892
Submitted by:	yuri@rawbw.com(maintainer)
23 May 2017 22:04:11
Original commit files touched by this commit  0.11.2.1
Revision:441555
joneum search for other commits by this committer
- Update to 0.11.2.1

PR:	219396
Submitted by:	Yuri Victorovich (Maintainer) <yuri@rawbw.com>
Approved by:	rene (mentor)
Differential Revision:	https://reviews.freebsd.org/D10856
07 May 2017 16:06:24
Original commit files touched by this commit  0.11.1
Revision:440347
miwi search for other commits by this committer
- Update to 0.11.1

PR:		219122
Submitted by:	maintainer
06 May 2017 06:05:24
Original commit files touched by this commit  0.11
Revision:440231
miwi search for other commits by this committer
pysam is a lightweight wrapper of the htslib C-API and provides facilities to
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
to the command line functionality of the samtools and bcftools packages. The
module supports compression and random access through indexing.

This module provides a low-level wrapper around the htslib C-API as using
cython and a high-level API for convenient access to the data within standard
genomic file formats.

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

PR:		218745
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

Number of commits found: 14

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