[khmer-announce] the khmer project v0.8 is released

Michael R. Crusoe mcrusoe at msu.edu
Thu Feb 27 14:01:58 PST 2014

Dear colleagues,

I am happy to announce version 0.8 of the khmer project.

89 changed files with 11,223 additions and 6,171 deletions.

## New functionality

Sparse graph labeling @camillescott ( sweep-reads-by-partition-buffered.py )
Initial support for Galaxy integration (for normalize-by-median and
abund-filter) @mr-c
Normalization of arguments across the scripts @camillescott

Note: The default branch on GitHub is now the 'master' branch. Our
unmaintained tutorials that install khmer with a plain git clone have a
warning added to them and potential user are directed to the
khmer-protocols: http://khmer-protocols.readthedocs.org

## Notable bugs fixed

load-graph gives erroneous memory estimate #279 @camillescott
If loadhash is specified, do not complain about hashsize #278 @RamRS
test_Hashbits case sensitivity #265 @luizirber
Installation fails: cannot find argparse >= 1.2.1 #258 @mr-c & @standage
Bugs found by coverity #256 @camillescott

## Minor updates

abundance-dist-single.py, abundance-dist.py, do-partition.py,
interleave-reads.py, load-graph.py, load-into-counting.py
normalize-by-median.py now exit with return code 1 instead of 255 as is
Program arguments that have default values are disclosed @mr-c
Developer documentation updates: contribution guidelines, coding standards,
code review hints (with checklist). Release instruction completely
Installation instructions tweaks including specific commands for Debian
derivatives and RHEL6.
Update to the latest versioneer.py & ez_setup.py
The latest version of setuptools is no longer required: version 0.6c11
appears to be just fine.
Many code cleanups. Python namespace usage was tidied. Type safety was
strengthened in the C++/Python integration.
Testing coverage measures the scripts properly.

## Known Issues

All of these are pre-existing.

Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in

Some FASTQ files confuse our parser when running with more than one thread.
For example, while using load-into-counting.py. If you experience this then
add "--threads=1" to your command line. This issue is being tracked in

If your hashfile gets truncated, perhaps from a full filesystem, then our
tools currently will get stuck. This is being tracked in

Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in

A user has reported a floating point exception when running
count-overlap.py. There is no workaround at this time.

## Contributors

@camillescott, @mr-c, @ctb, @luizirber, @RamRS, @humberto-ortiz, and
Special thanks to the new contributors!

Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
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